Publication Records

KANDRA, Mário, Tereza VÁŇOVÁ, Vincent Alexander JONGEN, Jakub POSPÍŠIL, Josef NOVAK, Václav CHOCHOLA, Tomas BURYSKA, Zbyněk PROKOP, Zdenek HODNY, Aleš HAMPL, Dáša BOHAČIAKOVÁ and Josef JAROŠ. A closed 3D printed microfluidic device for automated growth and differentiation of cerebral organoids from single-cell suspension. Biotechnology Journal. WEINHEIM: WILEY-V C H VERLAG GMBH, 2024, vol. 19, No 8, p. 1-17. ISSN 1860-6768. Available from: https://dx.doi.org/10.1002/biot.202400240.

KHAN, Rayyan Tariq, Petra POKORNÁ, Jan DVORSKÝ, Simeon BORKO, Ihor AREFIEV, Joan PLANAS IGLESIAS, Adam DOBIÁŠ, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Veronika SZOTKOWSKÁ, Jaroslav ŠTĚRBA, Ondřej SLABÝ, Jiří DAMBORSKÝ, Stanislav MAZURENKO and David BEDNÁŘ. A computational workflow for analysis of missense mutations in precision oncology. JOURNAL OF CHEMINFORMATICS. ENGLAND: BMC, 2024, vol. 16, No 1, p. 1-10. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-024-00876-3.

PLANAS IGLESIAS, Joan, Simeon BORKO, Jan SWIATKOWSKI, Matej ELIAS, Martin HAVLÁSEK, Ondrej SALAMON, Ekaterina GRAKOVA, Antonín KUNKA, Tomas MARTINOVIC, Jiří DAMBORSKÝ, Jan MARTINOVIC and David BEDNÁŘ. AggreProt: a web server for predicting and engineering aggregation prone regions in proteins. Nucleic Acids Research. Oxford: Oxford University Press, 2024, vol. 52, W1, p. "W159"-"W169", 11 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkae420.

SLÁNSKÁ, Michaela, Lenka ŠTACKOVÁ, Sérgio Manuel MARQUES, Peter ŠTACKO, Marek MARTÍNEK, Luboš JÍLEK, Martin TOUL, Jiří DAMBORSKÝ, David BEDNÁŘ, Petr KLÁN and Zbyněk PROKOP. Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2024, vol. 14, No 15, p. 11635-11645. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.4c03503.

FRUHAUF, Sebastian, Dominic PUHRINGER, Michaela THAMHESL, Patricia FAJTL, Elisavet KUNZ-VEKIRU, Andreas HOBARTNER-GUSSL, Gerd SCHATZMAYR, Gerhard ADAM, Jiří DAMBORSKÝ, Kristina DJINOVIC-CARUGO, Zbyněk PROKOP and Wulf-Dieter MOLL. Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2024, vol. 14, No 5, p. 3392-3410. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.4c00271.

VELECKÝ, Jan, Matej BEREZNÝ, Miloš MUSIL, Jiří DAMBORSKÝ, David BEDNÁŘ and Stanislav MAZURENKO. BenchStab: A tool for automated querying of web-based stability predictors. BIOINFORMATICS. ENGLAND: OXFORD UNIV PRESS, 2024, vol. 40, No 9, p. 1-5. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btae553.

DE LA BOURDONNAYE, Gabin, Tereza GHAZALOVÁ, Petr FOJTÍK, Katerina KUTALKOVA, David BEDNÁŘ, Jiří DAMBORSKÝ, Vladimír ROTREKL, Veronika STEPANKOVA and Radka CHALOUPKOVÁ. Computer-aided engineering of stabilized fibroblast growth factor 21. Computational and Structural Biotechnology Journal. Elsevier, 2024, vol. 23, December 2024, p. 942-951. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2024.02.001.

MARQUES, Sérgio Manuel, Petr KOUBA, Anthony Thomas P LEGRAND, Jiri SEDLAR, Lucas DISSON, Joan PLANAS IGLESIAS, Zainab Kemi SANUSI, Antonín KUNKA, Jiří DAMBORSKÝ, Tomas PAJDLA, Zbyněk PROKOP, Stanislav MAZURENKO, Josef SIVIC and David BEDNÁŘ. CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS AU. WASHINGTON: AMER CHEMICAL SOC, 2024, vol. 4, No 6, p. 2228-2245. ISSN 2691-3704. Available from: https://dx.doi.org/10.1021/jacsau.4c00182.

KNOZ, Martin, Jakub HOLOUBEK, Břetislav LIPOVÝ, Martin FALDYNA, Radka CHALOUPKOVÁ, Veronika PAVLINAKOVA, Johana MUCHOVA, Jana BRTNIKOVA, Jiří JARKOVSKÝ and Lucy VOJTOVA. Evaluation of viscoelastic parameters and photo-based assessment of newly developed dermal substitutes modified with thermostabilized fibroblast growth factor 2. Burns. London: ELSEVIER SCI LTD, 2024, vol. 50, No 6, p. 1586-1596. ISSN 0305-4179. Available from: https://dx.doi.org/10.1016/j.burns.2024.03.020.

MIČAN, Jan, Da 'san M. M. JARADAT, Weidong LIU, Gert WEBER, Stanislav MAZURENKO, Uwe T. BORNSCHEUER, Jiří DAMBORSKÝ, Ren WEI and David BEDNÁŘ. Exploring new galaxies: Perspectives on the discovery of novel PET-degrading enzymes. Applied Catalysis B: Environment and Energy. Amsterdam: Elsevier, 2024, vol. 342, March 2024, p. 1-16. ISSN 0926-3373. Available from: https://dx.doi.org/10.1016/j.apcatb.2023.123404.

MUSIL, Miloš, Andrej JEZIK, Jana HORÁČKOVÁ, Simeon BORKO, Petr KABOUREK, Jiří DAMBORSKÝ and David BEDNÁŘ. FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. Briefings in Bioinformatics. Oxford University Press, 2024, vol. 25, No 1, p. 1-10. ISSN 1467-5463. Available from: https://dx.doi.org/10.1093/bib/bbad425.

ŠPAČKOVÁ, Anna, Ondřej VÁVRA, Tomáš RAČEK, Václav BAZGIER, David SEHNAL, Jiří DAMBORSKÝ, Radka SVOBODOVÁ, David BEDNÁŘ and Karel BERKA. ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. Nucleic Acids Research. Oxford University Press, 2024, vol. 52, D1, p. "D413"-"D418", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkad1012.

PUSHKAROVA, Nadiia, Jana HENNELOVA, Sérgio Manuel MARQUES, David BEDNÁŘ, Kamil PARUCH, Naresh AKAVARAM, L. SPICHAL, Jiří DAMBORSKÝ, A. YEMETS and Jan HEJÁTKO. IDENTIFICATION OF NOVEL CYTOKININS BY MOLECULAR DOCKING. In IV Conference for Young Scientists “Plant biology and biotechnology”. 2024.

SCHÄFER, Marco, Nicolas BRICH, Jan BYŠKA, Sérgio Manuel MARQUES, David BEDNÁŘ, Philipp THIEL, Barbora KOZLÍKOVÁ and Michael KRONE. InVADo: Interactive Visual Analysis of Molecular Docking Data. IEEE Transactions on Visualization and Computer Graphics. IEEE Computer Society, 2024, vol. 30, No 4, p. 1984-1997. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2023.3337642.

VÁVRA, Ondřej, J. TYZACK, Faraneh HADDADI, Jan DVORSKÝ, Jiří DAMBORSKÝ, Stanislav MAZURENKO, J.M. THORNTON and David BEDNÁŘ. Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2024, vol. 16, No 1, p. 1-14. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-024-00907-z.

BUSHUIEV, Anton, Roman BUSHUIEV, Petr KOUBA, Anatolii FILKIN, Marketa GABRIELOVA, Michal GABRIEL, Jiri SEDLAR, Tomas PLUSKAL4, Jiří DAMBORSKÝ, Stanislav MAZURENKO and Josef SIVIC. Learning to design protein-protein interactions with enhanced generalization. Online. In 12th International Conference on Learning Representations 2024. 2024, 26 pp.

AKITA, Masaki, Paul GIRVAN, Mário ŠPÍREK, Jiří NOVÁČEK, David RUEDA, Zbyněk PROKOP and Lumír KREJČÍ. Mechanism of BCDX2-mediated RAD51 nucleation on short ssDNA stretches and fork DNA. Nucleic acids research. Oxford: Oxford University Press, 2024, 15 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkae770.

ŠTOURAČ, Jan, Simeon BORKO, Rayyan Tariq KHAN, Petra POKORNÁ, Adam DOBIÁŠ, Joan PLANAS IGLESIAS, Stanislav MAZURENKO, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Veronika SZOTKOWSKÁ, Jaroslav ŠTĚRBA, Ondřej SLABÝ, Jiří DAMBORSKÝ and David BEDNÁŘ. PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. Briefings in Bioinformatics. Oxford University Press, 2024, vol. 25, No 1, p. 1-10. ISSN 1467-5463. Available from: https://dx.doi.org/10.1093/bib/bbad441.

BUSHUIEV, Anton, Roman BUSHUIEV, Jiri SEDLAR, Tomas PLUSKAL, Jiří DAMBORSKÝ, Stanislav MAZURENKO and Josef SIVIC. Revealing data leakage in protein interaction benchmarks. In ICLR 2024 Workshop on Generative and Experimental Perspectives for Biomolecular Design. 2024, 13 pp.

OPÁLENÝ, Filip, Pavol ULBRICH, Joan PLANAS IGLESIAS, Jan BYŠKA, Jan ŠTOURAČ, David BEDNÁŘ, Katarína FURMANOVÁ and Barbora KOZLÍKOVÁ. Visual Support for the Loop Grafting Workflow on Proteins. IEEE Transactions on Visualization and Computer Graphics. United States: IEEE Computer Society, 2024. ISSN 1077-2626.

KUNKA, Antonín, Sérgio Manuel MARQUES, Martin HAVLÁSEK, Michal VAŠINA, Nikola VELÁTOVÁ, Lucia CENGELOVÁ, David KOVÁŘ, Jiří DAMBORSKÝ, Martin MAREK, David BEDNÁŘ and Zbyněk PROKOP. Advancing Enzyme's Stability and Catalytic Efficiency through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2023, vol. 13, No 19, p. 12506-12518. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.3c02575.

ŠNAJDAROVÁ, Karolína, Sérgio Manuel MARQUES, Jiří DAMBORSKÝ, David BEDNÁŘ and Martin MAREK. Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum. Acta Crystallographica Section D: Structural Biology. Chester: International Union of Crystallography, 2023, vol. 79, November, p. 956-970. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798323006642.

SMITH, Andrea, Martin TOUL, Daniel PLUSKAL, Racha BAATALLAH, Glwadys GAGNOT, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Vinicius T. T. SANTANA, Markéta STUCHLÁ, Petr NEUGEBAUER, Pimchai CHAIYEN, Jiří DAMBORSKÝ, David BEDNÁŘ, Yves L. L. JANIN, Zbyněk PROKOP and Martin MAREK. Catalytic mechanism for Renilla-type luciferases. Nature Catalysis. Nature Portfolio, 2023, vol. 6, No 1, p. 23-38. ISSN 2520-1158. Available from: https://dx.doi.org/10.1038/s41929-022-00895-z.

VILÍM, Jan, Tereza GHAZALOVÁ, Eliška PETULOVÁ, Aneta HORACKOVA, Veronika STEPANKOVA, Radka CHALOUPKOVÁ, David BEDNÁŘ, Jiří DAMBORSKÝ and Zbyněk PROKOP. Computer-assisted stabilization of fibroblast growth factor FGF-18. Computational and Structural Biotechnology Journal. AMSTERDAM: Elsevier, 2023, vol. 21, October 2023, p. 5144-5152. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2023.10.009.

GAO, Tadeja, Jiří DAMBORSKÝ, Yves L. JANIN and Martin MAREK. Deciphering Enzyme Mechanisms with Engineered Ancestors and Substrate Analogues. ChemCatChem. WEINHEIM: WILEY-V C H VERLAG GMBH, 2023, vol. 15, No 19, p. 1-16. ISSN 1867-3880. Available from: https://dx.doi.org/10.1002/cctc.202300745.

NEMERGUT, Michal, Sérgio Manuel MARQUES, Lukáš UHRÍK, Tereza VÁŇOVÁ, Markéta NEZVEDOVÁ, Darshak Chandulal GADARA, Durga JHA, Jan TULIS, Veronika NOVÁKOVÁ, Joan PLANAS IGLESIAS, Antonín KUNKA, Anthony Thomas P LEGRAND, Hana HŘÍBKOVÁ, Veronika POSPÍŠILOVÁ, Jiří SEDMÍK, Jan RAŠKA, Zbyněk PROKOP, Jiří DAMBORSKÝ, Dáša BOHAČIAKOVÁ, Zdeněk SPÁČIL, Lenka HERNYCHOVÁ, David BEDNÁŘ and Martin MAREK. Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer’s Disease drug candidate. Molecular Neurodegeneration. England: BMC, 2023, vol. 18, No 1, p. 1-25. ISSN 1750-1326. Available from: https://dx.doi.org/10.1186/s13024-023-00620-9.

ŠPAČKOVÁ, Anna, Ondřej VÁVRA, Tomáš RAČEK, Václav BAZGIER, David SEHNAL, Jiří DAMBORSKÝ, Radka SVOBODOVÁ and Karel BERKA. ChannelsDB 2.0: A Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era. In 3D-BioInfo | ICSB 3D-SIG | ELIXIR Czech Republic Community Meeting in Structural Bioinformatics. 2023.

TOUL, Martin, Veronika SLONKOVÁ, Jan MIČAN, Adam Paulin URMINSKÝ, Maria TOMKOVA, Erik SEDLÁK, David BEDNÁŘ, Jiří DAMBORSKÝ, Lenka HERNYCHOVÁ and Zbyněk PROKOP. Identification, characterization, and engineering of glycosylation in thrombolytics. Biotechnology Advances. OXFORD: Elsevier, 2023, vol. 66, September 2023, p. 1-23. ISSN 0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2023.108174.

NEMERGUT, Michal, Daniel PLUSKAL, Jana HORÁČKOVÁ, Tereza ŠUSTROVÁ, Jan TULIS, Tomáš BÁRTA, Racha BAATALLAH, Glwadys GAGNOT, Veronika NOVÁKOVÁ, Marika MAJEROVÁ, Karolina SEDLÁČKOVÁ, Sérgio Manuel MARQUES, Martin TOUL, Jiří DAMBORSKÝ, Zbyněk PROKOP, David BEDNÁŘ, Yves L. JANIN and Martin MAREK. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nature Communications. Berlin: Nature, 2023, vol. 14, No 1, p. 1-20. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-023-43403-y.

VAŠINA, Michal, David KOVÁŘ, Jiří DAMBORSKÝ, Ding YUN, Tianjin YANG, Andrew DE MELLO, Stanislav MAZURENKO, Stavros STAVRAKIS and Zbyněk PROKOP. In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning. Biotechnology Advances. OXFORD: Elsevier, 2023, vol. 66, September 2023, p. 1-22. ISSN 0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2023.108171.

KOUBA, Petr, Pavel KOHOUT, Faraneh HADDADI, Anton BUSHUIEV, Raman SAMUSEVICH, Jiri SEDLAR, Jiří DAMBORSKÝ, Tomáš PLUSKAL, Josef SIVIC and Stanislav MAZURENKO. Machine Learning-Guided Protein Engineering. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2023, vol. 13, No 21, p. 13863-13895. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.3c02743.

CHMELOVÁ, Klaudia, Tadeja GAO, Martin POLÁK, Andrea SMITH, Tristan I. CROLL, Tanvir SHAIKH, Jana ŠKAŘUPOVÁ, Radka CHALOUPKOVÁ, Kay DIEDERICHS, Randy J. READ, Jiří DAMBORSKÝ, Jiří NOVÁČEK and Martin MAREK. Multimeric structure of a subfamily III haloalkane dehalogenase-like enzyme solved by combination of cryo-EM and x-ray crystallography. Protein Science. Hoboken: Wiley, 2023, vol. 32, No 10, p. 1-22. ISSN 0961-8368. Available from: https://dx.doi.org/10.1002/pro.4751.

ČARNA, Maria, Isaac G. ONYANGO, Stanislav KATINA, Dušan HOLUB, Jan Sebastian NOVOTNY, Markéta NEZVEDOVÁ, Durga JHA, Zuzana NEDELSKA, Valentina LACOVICH, Thijs Vande VYVERE, Ruben HOUBRECHTS, Krystine GARCIA-MANSFIELD, Ritin SHARMA, Victoria DAVID-DIRGO, Martin VYHNALEK, Kateřina TEXLOVA, Hernan CHAVES, Nadine BAKKAR, Lucia PERTIERRA, Mojmír VINKLER, Hana MARKOVA, Jan LACZO, Kateřina SHEARDOVÁ, Marcela HORTOVA-KOHOUTKOVA, Jan FRIČ, Giancarlo FORTE, Petr KAŇOVSKY, Silvie BELAŠKOVA, Jiří DAMBORSKÝ, Jakub HORT, Nicholas T. SEYFRIED, Robert BOWSER, Gustavo SEVLEVER, Robert A. RISSMAN, Richard A. SMITH, Marian HAJDUCH, Patrick PIRROTTE, Zdeněk SPÁČIL, Eric B. DAMMER, Clara LIMBÄCK-STOKIN and Gorazd B. STOKIN. Pathogenesis of Alzheimer´s disease: Involvement of the choroid plexus. Alzheimer´s & Dementia. Wiley, 2023, vol. 19, No 8, p. 3537-3554. ISSN 1552-5260. Available from: https://dx.doi.org/10.1002/alz.12970.

BRHELOVÁ, Eliška, Veronika SLONKOVÁ, Martin TOUL, David KOVÁŘ, Sandra THALEROVÁ, Jana HLOŽKOVÁ, Peter SCHEER, Ahmet Davut AKSU, Radka OPATŘILOVÁ, Zbyněk PROKOP, Jiří DAMBORSKÝ and Robert MIKULÍK. Poměr plazminogen/plazmin jako ukazatel bezpečnosti trombolytické léčby (Plasminogen/plasmin ratio as safety indicator of thrombolytic treatment). In 50. pracovní konference "Komise experimentální kardiologie" 4.-6. října 2023, hotel Galant, Mikulov. 2023. ISBN 978-80-11-03840-3.

VÁVRA, Ondřej, Jakub BERANEK, Jan ŠTOURAČ, Martin SURKOVSKY, Jiří FILIPOVIČ, Jiří DAMBORSKÝ, Jan MARTINOVIC and David BEDNÁŘ. pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. Bioinformatics. Oxford: Oxford University Press, 2023, vol. 39, No 8, p. 1-3. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btad443.

PAPAGEORGIOU, Anna, Michaela POSPÍŠILOVÁ, Jakub CIBULKA, Raghib ASHRAF, Christopher WAUDBY, Pavel KADEŘÁVEK, Volha MAROZ, Karel KUBÍČEK, Zbyněk PROKOP, Lumír KREJČÍ and Konstantinos TRIPSIANES. Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase. Nature Communications. Berlin: Nature, 2023, vol. 14, No 1, p. 1-19. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-023-42503-z.

GOHL, Patrick, Jaume BONET, Oriol FORNES, Joan PLANAS IGLESIAS, Narcıs FERNANDEZ-FUENTES and Baldo OLIVA. SBILib: a handle for protein modeling and engineering. Bioinformatics. Oxford University Press, 2023, vol. 39, No 10, p. 1-3. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btad613.

ULBRICH, Pavol, Manuela WALDNER, Katarína FURMANOVÁ, Sérgio Manuel MARQUES, David BEDNÁŘ, Barbora KOZLÍKOVÁ and Jan BYŠKA. sMolBoxes: Dataflow Model for Molecular Dynamics Exploration. IEEE Transactions on Visualization and Computer Graphics. United States: IEEE Computer Society, 2023, vol. 29, No 1, p. 581-590. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2022.3209411.

LIPOVÝ, Břetislav, Martin KNOZ, Jakub HOLOUBEK, Eva HORÁLKOVÁ, Veronika PAVLIŇÁKOVÁ, Martin FALDYNA, Edita JEKLOVÁ, Radka CHALOUPKOVÁ, Zdeněk PAVLOVSKÝ, Irena KOUTNÁ and Lucy VOJTOVÁ. Stable Fibroblast Growth Factor 2 and its role in research from dermal regeneration to total skin substitute. In Recent Advances in Surgery and Burns, Kızılcahamam, Ankara, Turkey. 2023.

UHRIK, Lukas, Tomas HENEK, Joan PLANAS IGLESIAS, Josef KUCERA, Jiří DAMBORSKÝ, Martin MAREK and Lenka HERNYCHOVA. Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry. In Ângela Sousa, Luis Passarinha. Advanced Methods in Structural Biology. New York: Springer Nature, 2023, p. 293-318. 1. ISBN 978-1-0716-3146-1. Available from: https://dx.doi.org/10.1007/978-1-0716-3147-8_18.

PARUCH, Kamil, Benoit Jean-Pierre CARBAIN, Štěpán HAVEL, Jiří DAMBORSKÝ, Jan BREZOVSKÝ, Lukáš DANIEL, Alexandra SISÁKOVÁ, Fedor NIKULENKOV and Lumír KREJČÍ. Substituted aminothiazoles as inhibitors of nucleases. 2023.

PARUCH, Kamil, Benoit Jean-Pierre CARBAIN, Štěpán HAVEL, Jiří DAMBORSKÝ, Jan BREZOVSKÝ, Lukáš DANIEL, Alexandra SISÁKOVÁ, Fedor NIKULENKOV and Lumír KREJČÍ. Substituted aminothiazoles as inhibitors of nucleases. 2023.

HOLOUBEK, Jakub, Břetislav LIPOVÝ, Martin KNOZ, Tomáš KEMPNÝ, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ and Lucy VOJTOVÁ. The future for the application of fibroblast growth factor 2 in modern wound healing. BURNS. OXFORD: ELSEVIER SCI LTD, 2023, vol. 49, No 2, p. 484-486. ISSN 0305-4179. Available from: https://dx.doi.org/10.1016/j.burns.2022.10.007.

FULNEČEK, Jaroslav, Eva KLIMENTOVÁ, Albert CAIRO CALZADA, Soňa BUKOVČÁKOVÁ, Panagiotis ALEXIOU, Zbyněk PROKOP and Karel ŘÍHA. The SAP domain of Ku facilitates its efficient loading onto DNA ends. Nucleic Acids Research. Oxford: Oxford University Press, 2023, vol. 51, No 21, p. 11706-11716. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkad850.

DVOŘÁK, Petr, Pavel KREJČÍ, Lukáš BÁLEK, Lívia EISELLEOVÁ, Žaneta KONEČNÁ, Pavel DVOŘÁK, David BEDNÁŘ, Jan BREZOVSKÝ, Eva ŠEBESTOVÁ, Radka CHALOUPKOVÁ, Veronika ŠTĚPÁNKOVÁ, Pavel VAŇÁČEK, Zbyněk PROKOP, Jiří DAMBORSKÝ and Michaela BOSÁKOVÁ. Thermostable FGF2 polypeptide, use thereof. 2023.

DVOŘÁK, Petr, Pavel KREJČÍ, Lukáš BÁLEK, Lívia EISELLEOVÁ, Žaneta KONEČNÁ, Pavel DVOŘÁK, David BEDNÁŘ, Jan BREZOVSKÝ, Eva ŠEBESTOVÁ, Radka CHALOUPKOVÁ, Veronika ŠTĚPÁNKOVÁ, Pavel VAŇÁČEK, Zbyněk PROKOP, Jiří DAMBORSKÝ and Michaela BOSÁKOVÁ. Thermostable FGF2 polypeptide, use thereof. 2023.

DVOŘÁK, Petr, Pavel KREJČÍ, Lukáš BÁLEK, Lívia EISELLEOVÁ, Žaneta KONEČNÁ, Pavel DVOŘÁK, David BEDNÁŘ, Jan BREZOVSKÝ, Eva ŠEBESTOVÁ, Radka CHALOUPKOVÁ, Veronika ŠTĚPÁNKOVÁ, Pavel VAŇÁČEK, Zbyněk PROKOP, Jiří DAMBORSKÝ and Michaela BOSÁKOVÁ. Thermostable FGF2 Polypeptide, Use Thereof. 2023.

PARUCH, Kamil, Benoit Jean-Pierre CARBAIN, Štěpán HAVEL, Jiří DAMBORSKÝ, Jan BREZOVSKÝ, Lukáš DANIEL, Alexandra SISÁKOVÁ, Fedor NIKULENKOV and Lumír KREJČÍ. ヌクレアーゼの阻害剤としての置換アミノチアゾール (Substituted aminothiazoles as inhibitors of nucleases). 2022.

DVOŘÁK, Petr, Pavel KREJČÍ, Lukáš BÁLEK, Lívia EISELLEOVÁ, Žaneta KONEČNÁ, Pavel DVOŘÁK, David BEDNÁŘ, Jan BREZOVSKÝ, Eva ŠEBESTOVÁ, Radka CHALOUPKOVÁ, Veronika ŠTĚPÁNKOVÁ, Pavel VAŇÁČEK, Zbyněk PROKOP, Jiří DAMBORSKÝ and Michaela BOSÁKOVÁ. 熱安定性ＦＧＦ２ポリペプチド及びその使用 (Thermostable FGF2 polypeptide, use thereof). 2022.

PARDO, Isabel, David BEDNÁŘ, Patricia CALERO, Daniel C VOLKE, Jiří DAMBORSKÝ and Pablo I. NIKEL. A Nonconventional Archaeal Fluorinase Identified by In SilicoMining for Enhanced Fluorine Biocatalysis br. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2022, vol. 12, No 11, p. 6570-6577. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.2c01184.

VAŠINA, Michal, Pavel VAŇÁČEK, Jiri HON, David KOVÁŘ, Hana FALDYNOVÁ, Antonín KUNKA, Tomáš BURYŠKA, Christoffel P. S. BADENHORST, Stanislav MAZURENKO, David BEDNÁŘ, Stavros STAVRAKIS, Uwe T. BORNSCHEUER, Andrew DEMELLO, Jiří DAMBORSKÝ and Zbyněk PROKOP. Advanced database mining of efficient haloalkane dehalogenases by sequence and structure bioinformatics and microfluidics. Chem Catalysis. Elsevier, 2022, vol. 2, No 10, p. 2704-2725. ISSN 2667-1093. Available from: https://dx.doi.org/10.1016/j.checat.2022.09.011.

KUNKA, Antonín, David LACKO, Jan ŠTOURAČ, Jiří DAMBORSKÝ, Zbyněk PROKOP and Stanislav MAZURENKO. CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. Nucleic acids research. Oxford: Oxford University Press, 2022, vol. 50, W1, p. "W145"-"W151", 7 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkac378.

MUSIL, Miloš, Andrej JEŽÍK, Marie HAMŠÍKOVÁ, Jan ŠTOURAČ, Jakub GALGONEK, jiří VONDÁŠEK, David BEDNÁŘ and Jiří DAMBORSKÝ. Caver Web 1.2. 2022.

NIKITIN, Dmitri, Jan MIČAN, Martin TOUL, David BEDNÁŘ, Michaela PEŠKOVÁ, Patrícia KITTOVÁ, Sandra THALEROVÁ, Jan VÍTEČEK, Jiří DAMBORSKÝ, Robert MIKULÍK, Sarel J. FLEISHMAN, Zbyněk PROKOP and Martin MAREK. Computer-aided engineering of staphylokinase toward enhanced affinity and selectivity for plasmin. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2022, vol. 20, May 2022, p. 1366-1377. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2022.03.004.

ZÁMOCKÝ, Marcel, Miloš MUSIL, Maksym DANCHENKO, Peter FERIANC, Katarína CHOVANOVÁ, Peter BARÁTH, Andrej POLJOVKA and David BEDNÁŘ. Deep Insights into the Specific Evolution of Fungal Hybrid B Heme Peroxidases. BIOLOGY-BASEL. BASEL: MDPI, 2022, vol. 11, No 3, p. 1-18. ISSN 2079-7737. Available from: https://dx.doi.org/10.3390/biology11030459.

YANG, Tianjin, Alessia VILLOIS, Antonín KUNKA, Fulvio GRIGOLATO, Paolo AROSIO, Zbyněk PROKOP, Andrew DEMELLO and Stavros STAVRAKIS. Droplet-Based Microfluidic Temperature-Jump Platform for the Rapid Assessment of Biomolecular Kinetics. Analytical chemistry. American Chemical Society, 2022, vol. 94, No 48, p. 16675-16684. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.2c03009.

RAPP, Lea R., Sérgio Manuel MARQUES, Bernd NEBEL, Jiří DAMBORSKÝ and Bernhard HAUER. Engineering CYP153A(M.aq) to Oxyfunctionalize its Inhibitor Dodecylamine Using a LC/MS Based Rapid Flow Analysis Screening. ChemCatChem. WEINHEIM: WILEY-V C H VERLAG GMBH, 2022, vol. 14, No 6, p. 1-5. ISSN 1867-3880. Available from: https://dx.doi.org/10.1002/cctc.202101648.

TOUL, Martin, Dmitri NIKITIN, Martin MAREK, Jiří DAMBORSKÝ and Zbyněk PROKOP. Extended Mechanism of the Plasminogen Activator Staphylokinase Revealed by Global Kinetic Analysis: 1000-fold Higher Catalytic Activity than That of Clinically Used Alteplase. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2022, vol. 12, No 7, p. 3807-3814. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.1c05042.

VÁVRA, Ondřej, Jiří DAMBORSKÝ and David BEDNÁŘ. Fast approximative methods for study of ligand transport and rational design of improved enzymes for biotechnologies. Biotechnology Advances. Elsevier, 2022, vol. 60, November, p. 1-12. ISSN 0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2022.108009.

MUSIL, Miloš, Andrej JEŽÍK, Marie HAMŠÍKOVÁ, Jan ŠTOURAČ, Jakub GALGONEK, Saltuk Mustafa EYRILMEZ, Jiri VONDRASEK, Jiří DAMBORSKÝ and David BEDNÁŘ. Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web. Computational and Structural Biotechnology Journal. Elsevier, 2022, vol. 20, November 2022, p. 6512-6518. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2022.11.031.

POSPÍŠIL, Jakub, Milos HRABOVSKY, Dáša BOHAČIAKOVÁ, Zuzana HOVADKOVA, Miroslav JURÁSEK, Jarmila MLČOUŠKOVÁ, Kamil PARUCH, Šárka NEVOLOVÁ, Jiří DAMBORSKÝ, Aleš HAMPL and Josef JAROŠ. Geometric Control of Cell Behavior by Biomolecule Nanodistribution. ACS BIOMATERIALS SCIENCE & ENGINEERING. WASHINGTON: AMER CHEMICAL SOC, 2022, vol. 8, No 11, p. 4789-4806. ISSN 2373-9878. Available from: https://dx.doi.org/10.1021/acsbiomaterials.2c00650.

TOUL, Martin, Jan MIČAN, Veronika SLONKOVÁ, Dmitri NIKITIN, Martin MAREK, David BEDNÁŘ, Jiří DAMBORSKÝ and Zbyněk PROKOP. Hidden Potential of Highly Efficient and Widely Accessible Thrombolytic Staphylokinase. Stroke. Dallas: Lippincott Williams & Wilkins, 2022, vol. 53, No 10, p. 3235-3237. ISSN 0039-2499. Available from: https://dx.doi.org/10.1161/STROKEAHA.122.040219.

BOUCHALOVÁ, Pavla, Lucia SOMMEROVÁ, David POTĚŠIL, Andrea MARTIŠOVÁ, Petr LAPČÍK, Veronika BRYCHTOVÁ, Alexander SCHERL, Petr VOŇKA, Joan PLANAS IGLESIAS, Eric CHEVET, Pavel BOUCHAL and Roman HRSTKA. Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells. Molecular & Cellular Proteomics. American Society for Biochemistry and Molecular Biology, 2022, vol. 21, No 2, p. 1-19. ISSN 1535-9484. Available from: https://dx.doi.org/10.1016/j.mcpro.2021.100188.

DAVUT AKSU, Ahmet, Jana HLOŽKOVÁ, Peter SCHEER, Eliška BRHELOVÁ, Jan MIČAN, Martin TOUL, Jiří DAMBORSKÝ, Petr KAŠPÁREK, Jana DOLAŽALOVÁ and Robert MIKULÍK. IMPACT OF ADMINISTRATION METHOD OF THROMBOLYTICS ON THEIR THROMBOLYTIC EFFECTS. In Květinův Den 2022. 2022.

NEMERGUT, Michal, Tereza BÁŤKOVÁ, Dana VIGAŠOVÁ, Milan BARTOŠ, Martina HLOZANKOVA, Andrea SMITH, Barbora LIŠKOVÁ, Kateřina SHEARDOVÁ, Martin VYHNALEK, Jakub HORT, Jan LACZO, Ingrid KOVÁČOVÁ, Michal ŠITINA, Radoslav MATEJ, Radim JANČÁLEK, Martin MAREK and Jiří DAMBORSKÝ. Increased occurrence of Treponema spp. and double-species infections in patients with Alzheimer's disease. Science of the Total Environment. Amsterdam: Elsevier Science, 2022, vol. 844, October 2022, p. 1-7. ISSN 0048-9697. Available from: https://dx.doi.org/10.1016/j.scitotenv.2022.157114.

PLANAS IGLESIAS, Joan, Filip OPÁLENÝ, Pavol ULBRICH, Jan ŠTOURAČ, Zainab Kemi SANUSI, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Andrea SMITH, Jan BYŠKA, Jiří DAMBORSKÝ, Barbora KOZLÍKOVÁ and David BEDNÁŘ. LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic acids research. Oxford: Oxford University Press, 2022, vol. 50, W1, p. "W465"-"W473", 9 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkac249.

KOVÁŘ, David, Stanislav MAZURENKO, Jiří DAMBORSKÝ and Zbyněk PROKOP. MAPityser 2.1 - Analyzátor dat pro mikrofluidní platformu MAPit (MAPityser 2.1 - Data Analyser for the microfluidic platform MAPit). 2022.

WEI, Ren, Gerlis VON HAUGWIT, Lara PFAFF, Jan MIČAN, Christoffel P. S. BADENHORST, Weidong LIU, Gert WEBER, Harry P. AUSTIN, David BEDNÁŘ, Jiří DAMBORSKÝ and Uwe T. BORNSCHEUER. Mechanism-Based Design of Efficient PET Hydrolases. ACS Catalysis. American Chemical Society, 2022, vol. 12, No 6, p. 3382-3396. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.1c05856.

MARQUES, Sérgio Manuel, Michaela SLÁNSKÁ, Klaudia CHMELOVÁ, Radka CHALOUPKOVÁ, Martin MAREK, Spencer CLARK, Jiří DAMBORSKÝ, Eric T. KOOL, David BEDNÁŘ and Zbyněk PROKOP. Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling. JACS AU. WASHINGTON: AMER CHEMICAL SOC, 2022, vol. 2, No 6, p. 1324-1337. ISSN 2691-3704. Available from: https://dx.doi.org/10.1021/jacsau.2c00002.

PRAKINEE, Kridsadakorn, Aisaraphon PHINTHA, Surawit VISITSATTHAWONG, Narin LAWAN, Jeerus SUCHARITAKUL, Chadaporn KANTIWIRIYAWANITCH, Jiří DAMBORSKÝ, Penchit CHITNUMSUB, Van Pee KARL-HEINZ and Pimchai CHAIYEN. Mechanism-guided tunnel engineering to increase the efficiency of a flavin-dependent halogenase. NATURE CATALYSIS. ENGLAND: NATURE PORTFOLIO, 2022, vol. 5, No 6, p. 534-544. ISSN 2520-1158. Available from: https://dx.doi.org/10.1038/s41929-022-00800-8.

KOVÁŘ, David, Stanislav MAZURENKO, Michal VAŠINA, Jiří DAMBORSKÝ and Zbyněk PROKOP. MicroPEX Data Analyser 1.0* (MicroPEX Data Analyser 1.0). 2022.

KŘIVÁNEK, Jan, Marcel SCHÜLLER, Zuzana MARINČÁK VRANKOVÁ, Hana PÁLOVÁ, Ondřej SLABÝ, Radka CHALOUPKOVÁ, Petr NICKL, Petr KAŠPÁREK, Jan PROCHÁZKA, Radislav SEDLÁČEK and Petra BOŘILOVÁ LINHARTOVÁ. Modelling of a rare mutation in the GALNT3 gene found in patient with teeth and bone defects using genetically engineered mice. In 4th CPP Phenogenomics conference 2022. 2022.

PFAFF, Lara, Jian GAO, Zhishuai LI, Anna JAECKERING, Gert WEBER, Jan MIČAN, Yinping CHEN, Weiliang DONG, Xu HAN, Christian G. FEILER, Yu-Fei AO, Christoffel P. S. BADENHORST, David BEDNÁŘ, Gottfried J. PALM, Michael LAMMERS, Jiří DAMBORSKÝ, Birgit STRODEL, Weidong LIU, Uwe T. BORNSCHEUER and Ren WEI. Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase. ACS Catalysis. American Chemical Society, 2022, vol. 12, No 15, p. 9790-9800. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.2c02275.

PLANAS IGLESIAS, Joan, Filip OPÁLENÝ, Pavol ULBRICH, Jan ŠTOURAČ, Zainab Kemi SANUSI, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, A. SCHENKMAYEROVÁ, Jan BYŠKA, Jiří DAMBORSKÝ, Barbora KOZLÍKOVÁ and David BEDNÁŘ. Nástroj LoopGrafter (LoopGrafter software tool). 2022.

VARADI, Mihaly, Stephen ANYANGO, David ARMSTRONG, John BERRISFORD, Preeti CHOUDHARY, Mandar DESHPANDE, Nurul NADZIRIN, Sreenatha S. NAIR, Lukas PRAVDA, Ahsan TANWEER, Bissan AL-LAZIKANI, Claudia ANDREINI, Geoffrey J. BARTON, David BEDNÁŘ, Karel BERKA, Tom BLUNDELL, Kelly P. BROCK, Jose MARIA CARAZO, Jiří DAMBORSKÝ, Alessia DAVID, Sucharita DEY, Roland DUNBRACK, Fernandez Juan RECIO, Franca FRATERNALI, Toby GIBSON, Manuela HELMER-CITTERICH, David HOKSZA, Thomas HOPF, David JAKUBEC, Natarajan KANNAN, Radoslav KRIVAK, Manjeet KUMAR, Emmanuel D. LEVY, Nir LONDON, Jose Ramon MACIAS, Madhusudhan M. SRIVATSAN, Debora S. MARKS, Lennart MARTENS, Stuart A. MCGOWAN, Jake E. MCGREIG, Vivek MODI, Gonzalo R. PARRA, Gerardo PEPE, Damiano PIOVESAN, Jaime PRILUSKY, Valeria PUTIGNANO, Leandro G. RADUSKY, Pathmanaban RAMASAMY, Atilio O. RAUSCH, Nathalie REUTER, Luis A. RODRIGUEZ, Nathan J. ROLLINS, Antonio ROSATO, Luis SERRANO, Gulzar SINGH, Petr SKODA, Carlos Oscar S. SORZANO, Jan ŠTOURAČ, Joanna I. SULKOWSKA, Radka SVOBODOVÁ, Natalia TICHSHENKO, Silvio C. E. TOSATTO, Wim VRANKEN, Mark N. WASS, Dandan XUE, Daniel ZAIDMAN, Janet THORNTON, Michael STERNBERG, Christine ORENGO and Sameer VELANKAR. PDBe-KB: collaboratively defining the biological context of structural data. Nucleic acids research. Oxford: Oxford University Press, 2022, vol. 50, D1, p. "D534"-"D542", 9 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkab988.

ŠTOURAČ, Jan, Rayyan Tariq KHAN, Simeon BORKO, Petra POKORNÁ, Adam DOBIÁŠ, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Jaroslav ŠTĚRBA, Ondřej SLABÝ, Jiří DAMBORSKÝ and David BEDNÁŘ. PredictSNP Onco 1.0. 2022.

VELECKÝ, Jan, Marie HAMŠÍKOVÁ, Jan ŠTOURAČ, Miloš MUSIL, Jiří DAMBORSKÝ, David BEDNÁŘ and Stanislav MAZURENKO. SoluProtMutDB: A manually curated database of protein solubility changes upon mutations. Computational and Structural Biotechnology Journal. Elsevier, 2022, vol. 20, November 2022, p. 6339-6347. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2022.11.009.

VON HAUGWITZ, Gerlis, Xu HAN, Lara PFAFF, Qian LI, Hongli WEI, Jian GAO, Karen METHLING, Yufei AO, Yannik BRACK, Jan MIČAN, Christian G FEILER, Manfred S WEISS, David BEDNÁŘ, Gottfried J. PALM, Michael LALK, Michael LAMMERS, Jiří DAMBORSKÝ, Gert WEBER, Weidong LIU, Uwe T. BORNSCHEUER and Ren WEI. Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization. ACS Catalysis. American Chemical Society, 2022, vol. 12, No 24, p. 15259-15270. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.2c03772.

PARUCH, Kamil, Benoit Jean-Pierre CARBAIN, Štěpán HAVEL, Jiří DAMBORSKÝ, Jan BREZOVSKÝ, Lukáš DANIEL, Alexandra SISÁKOVÁ, Fedor NIKULENKOV and Lumír KREJČÍ. Substituted aminothiazoles as inhibitors of nucleases. 2022.

VAŠINA, Michal, Jan VELECKÝ, Joan PLANAS IGLESIAS, Sérgio Manuel MARQUES, Jana ŠKAŘUPOVÁ, Jiří DAMBORSKÝ, David BEDNÁŘ, Stanislav MAZURENKO and Zbyněk PROKOP. Tools for computational design and high-throughput screening of therapeutic enzymes. ADVANCED DRUG DELIVERY REVIEWS. NETHERLANDS: ELSEVIER, 2022, vol. 183, April 2022, p. 1-16. ISSN 0169-409X. Available from: https://dx.doi.org/10.1016/j.addr.2022.114143.

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Natalie M. HENDRIKSE, Jan ŠTOURAČ, Jiří DAMBORSKÝ and David BEDNÁŘ. Virtual screening of potential anticancer drugs based on microbial products. Seminars in Cancer Biology. London: Academic Press Ltd.-Elsevier Science Ltd., 2022, vol. 86, November 2022, p. 1207-1217. ISSN 1044-579X. Available from: https://dx.doi.org/10.1016/j.semcancer.2021.07.012.

KNOZ, Martin, Břetislav LIPOVÝ, Lucy VOJTOVÁ, Jakub HOLOUBEK, Jan ŽÍDEK, Johana BABRNÁKOVÁ, Lucie VIŠTEJNOVÁ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Jiří DAMBORSKÝ and Vanessa HEARNDEN. Collagen/Chitosan dermal substitute enriched by hyperstable FGF2, 4 years of development. In 12th EPSRC Meeting 27th - 28th August 2021, Turku, Finland. 2021.

PLANAS IGLESIAS, Joan, Sérgio Manuel MARQUES, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Miloš MUSIL, Jan ŠTOURAČ, Jiří DAMBORSKÝ and David BEDNÁŘ. Computational design of enzymes for biotechnological applications. Biotechnology Advances. OXFORD: Elsevier, 2021, vol. 47, March–April, p. 1-22. ISSN 0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2021.107696.

DAMBORSKÝ, Jiří, David BEDNÁŘ, Zbyněk PROKOP, Martin MAREK, Stanislav MAZURENKO, Jan ŠTOURAČ, Sérgio Manuel MARQUES, Gabriela Filipa FONSECA PINTO, Joan PLANAS IGLESIAS, Miloš MUSIL, Jiří HON, Ondřej VÁVRA, Rayyan Tariq KHAN, Jiří FILIPOVIČ and Barbora KOZLÍKOVÁ. Computational enzyme design for metabolic engineering. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

MARKOVÁ, Klára, Antonín KUNKA, Klaudia CHMELOVÁ, Martin HAVLÁSEK, Petra BABKOVÁ, Sérgio Manuel MARQUES, Michal VAŠINA, Joan PLANAS IGLESIAS, Radka CHALOUPKOVÁ, David BEDNÁŘ, Zbyněk PROKOP, Jiří DAMBORSKÝ and Martin MAREK. Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2021, vol. 11, No 21, p. 12864-12885. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.1c03343.

IERMAK, Iuliia, Oksana DEGTJARIK, Petra HAVLICKOVA, Michal KUTY, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Tanyana PRUDNIKOVA and Ivana KUTA SMATANOVA. Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum. Catalysts. Basel: MDPI, 2021, vol. 11, No 1, p. 1-15. ISSN 2073-4344. Available from: https://dx.doi.org/10.3390/catal11010005.

MAREK, Martin, Jiří DAMBORSKÝ, David BEDNÁŘ, Daniel PLUSKAL, Marika MAJEROVÁ and Joan PLANAS IGLESIAS. Designované a syntetizované geny kódující nově zkonstruované proteinové katalyzátory (luciferázy) s ověřenými vlastnostmi (Designed and synthesized genes coding for new luciferase enzymes with confirmed properties). 2021.

NIKITIN, Dmitri, Seungbum CHOI, Jan MIČAN, Martin TOUL, Wi-Sun RYU, Jiří DAMBORSKÝ, Robert MIKULÍK and Dong-Eog KIM. Development and Testing of Thrombolytics in Stroke. JOURNAL OF STROKE. SEOUL: KOREAN STROKE SOC, 2021, vol. 23, No 1, p. 12-36. ISSN 2287-6391. Available from: https://dx.doi.org/10.5853/jos.2020.03349.

TOUL, Martin, Andrea SMITH, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Martin MAREK, Lenka HERNYCHOVÁ, Veronika LIŠKOVÁ, Daniel PLUSKAL, Stephane EMOND, Mark DÖRR, Joan PLANAS IGLESIAS, Radka CHALOUPKOVÁ, David BEDNÁŘ, Zbyněk PROKOP, Uwe T. BORNSCHEUER, Florian HOLLFELDER and Jiří DAMBORSKÝ. Engineering protein dynamics for the understanding of divergent evolution of the Renilla luciferase. In The 45th FEBS Congress. 2021. ISSN 2211-5463.

SCHENKMAYEROVÁ, Andrea, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Martin TOUL, Martin MAREK, Lenka HERNYCHOVÁ, Joan PLANAS IGLESIAS, Veronika LIŠKOVÁ, Daniel PLUSKAL, Michal VAŠINA, Stephane EMOND, Mark DÖRR, Radka CHALOUPKOVÁ, David BEDNÁŘ, Zbyněk PROKOP, Florian HOLLFELDER, Uwe T. BORNSCHEUER and Jiří DAMBORSKÝ. Engineering the protein dynamics of an ancestral luciferase. Nature Communications. London: Nature Publishing Group, 2021, vol. 12, No 1, p. 3616-3631. ISSN 2041-1723. Available from: https://dx.doi.org/10.1038/s41467-021-23450-z.

HESS, David, Veronika DOČKALOVÁ, Piia Pauliina KOKKONEN, David BEDNÁŘ, Jiří DAMBORSKÝ, Andrew DEMELLO, Zbyněk PROKOP and Stavros STAVRAKIS. Exploring mechanism of enzyme catalysis by on-chip transient kinetics coupled with global data analysis and molecular modeling. Chem. Cambridge: Cell Press, 2021, vol. 7, No 4, p. 1066-1079. ISSN 2451-9294. Available from: https://dx.doi.org/10.1016/j.chempr.2021.02.011.

MUSIL, Miloš, Rayyan Tariq KHAN, Andy BEIER, Jan ŠTOURAČ, Hannes KONEGGER, Jiří DAMBORSKÝ and David BEDNÁŘ. FireProt(ASR): A Web Server for Fully Automated Ancestral Sequence Reconstruction. Briefings in Bioinformatics. OXFORD: Oxford University Press, 2021, vol. 22, No 4, p. 1-11. ISSN 1467-5463. Available from: https://dx.doi.org/10.1093/bib/bbaa337.

ŠTOURAČ, Jan, Juraj DUBRAVA, Miloš MUSIL, Jana HORÁČKOVÁ, Jiří DAMBORSKÝ, Stanislav MAZURENKO and David BEDNÁŘ. FireProt(DB): database of manually curated protein stability data. Nucleic acids research. Oxford: Oxford University Press, 2021, vol. 49, D1, p. "D319"-"D324", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkaa981.

KHAN, Rayyan Tariq, Miloš MUSIL, Jan DVORSKÝ, Jiří DAMBORSKÝ and David BEDNÁŘ. Fully Automated Ancestral Sequence Reconstruction using FireProtASR. Current Protocols. Wiley, 2021, vol. 1, No 2, p. e30, 13 pp. ISSN 2691-1299. Available from: https://dx.doi.org/10.1002/cpz1.30.

MIRELA-BOTA, Patricia, Joaquim AGUIRRE-PLANS, Alberto MESEGUER, Cristiano GALLETTI, Joan SEGURA, Joan PLANAS IGLESIAS, Javi GARCIA-GARCIA, Emre GUNEY, Baldo OLIVA and Narcis FERNANDEZ-FUENTES. Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein–Protein Interaction Data. Journal of Molecular Biology. London: Elsevier Science Ltd, 2021, vol. 433, No 11, p. 166656-166666. ISSN 0022-2836. Available from: https://dx.doi.org/10.1016/j.jmb.2020.09.015.

VIGAŠOVÁ, Dana, Michal NEMERGUT, Barbora LIŠKOVÁ and Jiří DAMBORSKÝ. Multi-pathogen infections and Alzheimer's disease. Microbial Cell Factories. London: BioMed Central Ltd, 2021, vol. 20, No 1, p. 25-37. ISSN 1475-2859. Available from: https://dx.doi.org/10.1186/s12934-021-01520-7.

SCHUITEN, Eva D., Christoffel P. S. BADENHORST, Gottfried J. PALM, Leona BERNDT, Michael LAMMERS, Jan MIČAN, David BEDNÁŘ, Jiří DAMBORSKÝ and Uwe T. BORNSCHEUER. Promiscuous Dehalogenase Activity of the Epoxide Hydrolase CorEH from Corynebacterium sp. C12. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2021, vol. 11, No 10, p. 6113-6120. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.1c00851.

MARQUES, Sérgio Manuel, Lucie ŠUPOLÍKOVÁ, Lenka MOLČANOVÁ, Karel ŠMEJKAL, David BEDNÁŘ and Iva SLANINOVÁ. Screening of Natural Compounds as P-Glycoprotein Inhibitors against Multidrug Resistance. BIOMEDICINES. BASEL: MDPI, 2021, vol. 9, No 4, p. 1-22. ISSN 2227-9059. Available from: https://dx.doi.org/10.3390/biomedicines9040357.

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Ondřej VÁVRA, Sérgio Manuel MARQUES, Jiří FILIPOVIČ, David BEDNÁŘ and Jiří DAMBORSKÝ. Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2021, vol. 19, May, p. 3187-3197. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2021.05.043.

HOZZOVÁ, Jana, Ondřej VÁVRA, David BEDNÁŘ and Jiří FILIPOVIČ. Simulation of Ligand Transport in Receptors Using CaverDock. In Flavio Ballante. Protein-Ligand Interactions and Drug Design. New York: Humana, New York, NY, 2021, p. 105-124. Methods in Molecular Biology, vol 2266. ISBN 978-1-0716-1208-8. Available from: https://dx.doi.org/10.1007/978-1-0716-1209-5_6.

HON, Jiří, Martin MARUSIAK, Tomas MARTINEK, Antonín KUNKA, Jaroslav ZENDULKA, David BEDNÁŘ and Jiří DAMBORSKÝ. SoluProt: prediction of soluble protein expression in Escherichia coli. Bioinformatics. Oxford: Oxford University Press, 2021, vol. 37, No 1, p. 23-28. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btaa1102.

SHAPOSHNIKOVA, Anastasiia, Michal KUTY, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Ivana KUTA SMATANOVA, Babak MINOFAR and Tanyana PRUDNIKOVA. Stabilization of Haloalkane Dehalogenase Structure by Interfacial Interaction with Ionic Liquids. Crystals. MDPI, 2021, vol. 11, No 9, p. 1-16. ISSN 2073-4352. Available from: https://dx.doi.org/10.3390/cryst11091052.

MAZUR, Andrii, Pavel GRINKEVICH, Radka CHALOUPKOVÁ, Petra HAVLICKOVA, Barbora KASCAKOVA, Michal KUTY, Jiří DAMBORSKÝ, Ivana KUTA SMATANOVA and Tatyana PRUDNIKOVA. Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA. International Journal of Molecular Sciences. Basel: Multidisciplinary Digital Publishing Institute, 2021, vol. 22, No 21, p. 1-14. ISSN 1422-0067. Available from: https://dx.doi.org/10.3390/ijms222111992.

GORECKI, Lukas, Anna MISIACHNA, Jiří DAMBORSKÝ, Rafael DOLEZAL, Jan KORABECNY, Lada CEJKOVA, Kristina HAKENOVA, Marketa CHVOJKOVA, Jana KARASOVA ZDAROVA, Lukas PRCHAL, Martin NOVAK, Marharyta KOLCHEVA, Stepan KORTUS, Karel VALES, Martin HORAK and Ondřej SOUKUP. Structure-activity relationships of dually-acting acetylcholinesterase inhibitors derived from tacrine on N-methyl-D-Aspartate receptors. European Journal of Medicinal Chemistry. PARIS: ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER, 2021, vol. 219, July 2021, p. 1-16. ISSN 0223-5234. Available from: https://dx.doi.org/10.1016/j.ejmech.2021.113434.

PARUCH, Kamil, Benoit Jean-Pierre CARBAIN, Štěpán HAVEL, Jiří DAMBORSKÝ, Jan BREZOVSKÝ, Lukáš DANIEL, Alexandra SISÁKOVÁ, Fedor NIKULENKOV and Lumír KREJČÍ. SUBSTITUTED AMINOTHIAZOLES AS INHIBITORS OF NUCLEASES. 2021.

RAPP, Lea R., Sérgio Manuel MARQUES, Erna ZUKIC, Benjamin ROWLINSON, Mahima SHARMA, Gideon GROGAN, Jiří DAMBORSKÝ and Bernhard HAUER. Substrate Anchoring and Flexibility Reduction in CYP153A(M.aq) Leads to Highly Improved Efficiency toward Octanoic Acid. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2021, vol. 11, No 5, p. 3182-3189. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.0c05193.

KOKKONEN, Piia Pauliina, Andy BEIER, Stanislav MAZURENKO, Jiří DAMBORSKÝ, David BEDNÁŘ and Zbyněk PROKOP. Substrate inhibition by the blockage of product release and its control by tunnel engineering. RSC Chemical Biology. Cambridge: Royal Society of Chemistry, 2021, vol. 2, No 2, p. 645-655. ISSN 2633-0679. Available from: https://dx.doi.org/10.1039/d0cb00171f.

MAZUR, Andrii, Tanyana PRUDNIKOVA, Pavel GRINKEVICH, Jeroen R. MESTERS, Daria MRAZOVA, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Michal KUTY, Petr KOLENKO and Ivana KUTA SMATANOVA. The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2. Acta Crystallographica Section D: Structural Biology. Chester: International Union of Crystallography, 2021, vol. 77, March 2021, p. 347-356. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798321000486.

DVOŘÁK, Petr, Pavel KREJČÍ, Lukáš BÁLEK, Lívia EISELLEOVÁ, Žaneta KONEČNÁ, Pavel DVOŘÁK, David BEDNÁŘ, Jan BREZOVSKÝ, Eva ŠEBESTOVÁ, Radka CHALOUPKOVÁ, Veronika ŠTĚPÁNKOVÁ, Pavel VAŇÁČEK, Zbyněk PROKOP, Jiří DAMBORSKÝ and Michaela BOSÁKOVÁ. Thermostable FGF2 polypeptide, use thereof. 2021.

DVOŘÁK, Petr, Pavel KREJČÍ, Lukáš BÁLEK, Lívia EISELLEOVÁ, Žaneta KONEČNÁ, Pavel DVOŘÁK, David BEDNÁŘ, Jan BREZOVSKÝ, Eva ŠEBESTOVÁ, Radka CHALOUPKOVÁ, Veronika ŠTĚPÁNKOVÁ, Pavel VAŇÁČEK, Zbyněk PROKOP, Jiří DAMBORSKÝ and Michaela BOSÁKOVÁ. Thermostable FGF2 Polypeptide, Use Thereof. 2021.

KNOZ, Martin, Břetislav LIPOVÝ, Jakub HOLOUBEK, Jan ŽÍDEK, Johana BABRNÁKOVÁ, Veronika PAVLIŇÁKOVÁ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GOPFERT, Jiří DAMBORSKÝ, Vanessa HEARNDEN, Lucy VOJTOVÁ and Michaela CVANOVÁ. Vývoj dermální náhrady, kvalitativní testování na zvířecích modelech. In II. Česko-slovenský kongres "Mezioborové přístupy v hojení ran". 2021.

MARQUES, Sérgio Manuel, Joan PLANAS IGLESIAS and Jiří DAMBORSKÝ. Web-based tools for computational enzyme design. Current Opinion in Structural Biology. London: Elsevier Science Ltd., 2021, vol. 69, August 2021, p. 19-34. ISSN 0959-440X. Available from: https://dx.doi.org/10.1016/j.sbi.2021.01.010.

CHMELOVÁ, Klaudia, Eva ŠEBESTOVÁ, Veronika LIŠKOVÁ, Andy BEIER, David BEDNÁŘ, Zbyněk PROKOP, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. A Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique (S)-Enantiopreference, and High Thermostability. Applied and Environmental Microbiology. Washington, D.C.: American Society for Microbiology, 2020, vol. 86, No 17, p. 1-12. ISSN 0099-2240. Available from: https://dx.doi.org/10.1128/AEM.02820-19.

KUMAR, Lokender, Joan PLANAS IGLESIAS, Chase HARMS, Sumaer KAMBOJ, Derek WRIGHT, Judith KLEIN-SEETHARAMAN and K.Susanta SARKAR. Activity-dependent interdomain dynamics of matrix metalloprotease-1 on fibrin. Scientific Reports. Berlin: Nature Research, 2020, vol. 10, No 1, p. 1-14. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-020-77699-3.

KUMAR, Lokender, Anthony NASH, Chase HARMS, Joan PLANAS IGLESIAS, Derek WRIGHT, Judith KLEIN-SEETHARAMAN and Susanta K SARKAR. Allosteric Communications between Domains Modulate the Activity of Matrix Metalloprotease-1. Biophysical Journal. Bethesda, USA: Biophysical Society, 2020, vol. 119, No 2, p. 360-374. ISSN 0006-3495. Available from: https://dx.doi.org/10.1016/j.bpj.2020.06.010.

ASLAN-UZEL, Askin S., Andy BEIER, David KOVÁŘ, Clemens CZIEGLER, Santosh K. PADHI, Eva D. SCHUITEN, Mark DORR, Dominique BOTTCHER, Frank HOLLMANN, Florian RUDROFF, Marko D. MIHOVILOVIC, Tomáš BURYŠKA, Jiří DAMBORSKÝ, Zbyněk PROKOP, Christoffel P. S. BADENHORST and Uwe T. BORNSCHEUER. An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation. ChemCatChem. WEINHEIM: WILEY-V C H VERLAG GMBH, 2020, vol. 12, No 7, p. 2032-2039. ISSN 1867-3880. Available from: https://dx.doi.org/10.1002/cctc.201901891.

FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE/ACM Transactions on Computational Biology and Bioinformatics. Los Alamitos: IEEE Computer Society, 2020, vol. 17, No 5, p. 1625-1638. ISSN 1545-5963. Available from: https://dx.doi.org/10.1109/TCBB.2019.2907492.

LIPOVÝ, Břetislav, Lucy VOJTOVÁ, Veronika ŠTĚPÁNKOVÁ, Jakub HOLOUBEK, Martin KNOZ, Radka CHALOUPKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT and Vanessa HEARNDEN. Current status and future perspectives of fibroblast growth factor 2 in wound healing. In 6th CONGRESS OF WUWHS. 2020.

SEDLÁČKOVÁ, Jitka and Kenneth HOLMQVIST. Deaf learners' processing of English textbook material : An eye-tracking study. In 11th Brno International Conference of English, American and Canadian Studies : "Breaking the Boundaries : In Between Texts, Cultures and Conventions", 12–14 February, 2020, Brno, Faculty of Arts, Masaryk University. 2020.

MARKOVÁ, Klára, Klaudia CHMELOVÁ, Sérgio Manuel MARQUES, Philippe CARPENTIER, David BEDNÁŘ, Jiří DAMBORSKÝ and Martin MAREK. Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chemical Science. Cambridge: Royal Society of Chemistry, 2020, vol. 11, No 41, p. 11162-11178. ISSN 2041-6520. Available from: https://dx.doi.org/10.1039/d0sc03367g.

FURMANOVÁ, Katarína, Ondřej VÁVRA, Barbora KOZLÍKOVÁ, Jiří DAMBORSKÝ, Vojtěch VONÁSEK, David BEDNÁŘ and Jan BYŠKA. DockVis: Visual Analysis of Molecular Docking Trajectories. Computer Graphics Forum. Wiley-Blackwell, 2020, vol. 39, No 6, p. 452-464. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.14048.

HON, Jiří, Simeon BORKO, Jan ŠTOURAČ, Zbyněk PROKOP, Jaroslav ZENDULKA, David BEDNÁŘ, Tomas MARTINEK and Jiří DAMBORSKÝ. EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. Nucleic acids research. Oxford: Oxford University Press, 2020, vol. 48, W1, p. "W104"-"W109", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkaa372.

VAŠINA, Michal, Pavel VAŇÁČEK, Jiří DAMBORSKÝ and Zbyněk PROKOP. Exploration of enzyme diversity: High-throughput techniques for protein production and microscale biochemical characterization. Online. In Dan S. Tawfik. Methods in Enzymology - Enzyme Engineering and Evolution: General Methods. Neuveden: Elsevier Inc, 2020, p. 51-85. ISBN 978-0-12-821149-6. Available from: https://dx.doi.org/10.1016/bs.mie.2020.05.004.

DOČKALOVÁ, Veronika, Esther Maria MARQUEZ SANCHEZ - CARNERERO, Zuzana DUNAJOVÁ, Eduardo PALAO UTIEL, Michaela SLÁNSKÁ, Tomáš BURYŠKA, Jiří DAMBORSKÝ, Petr KLÁN and Zbyněk PROKOP. Fluorescent substrates for haloalkane dehalogenases: Novel probes for mechanistic studies and protein labeling. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2020, vol. 18, No 2020, p. 922-932. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2020.03.029.

TÓTHOVÁ, Lenka and Jitka SEDLÁČKOVÁ. Fostering autonomy in learners with special needs: a specialized e-learning course. In CercleS 2020. Language Centres at a Crossroads: Open Directions for New Generations of Learners. 2020.

MAZURENKO, Stanislav, Zbyněk PROKOP and Jiří DAMBORSKÝ. Machine Learning in Enzyme Engineering. ACS Catalysis. Washington, D.C.: American Chemical Society, 2020, vol. 10, No 2, p. 1210-1223. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.9b04321.

TÓTHOVÁ, Lenka, Jitka SEDLÁČKOVÁ and Eva BARNOVÁ. Online English for International Mobilities: A course for students. In The LangSkills project closing conference. 2020.

LABUDOVÁ, Dominika, Jiří HON and Matej LEXA. pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. Bioinformatics. Oxford: Oxford University Press, 2020, vol. 36, No 8, p. 2584-2586. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz928.

TÓTHOVÁ, Lenka, Jitka SEDLÁČKOVÁ and Eva BARNOVÁ. Seminář pro učitele angličtiny pracující s neslyšícími a nedoslýchavými studenty (Seminar for English teachers working with Deaf, deaf and hard of hearing students). 2020.

MAREK, Martin, Radka CHALOUPKOVÁ, Tanyana PRUDNIKOVA, Yukari SATO, Pavlina REZACOVA, Yuji NAGATA, Ivana SMATANOVA KUTA and Jiří DAMBORSKÝ. Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2020, vol. 18, December 2020, p. 1352-1362. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2020.05.019.

BABKOVÁ, Petra, Zuzana DUNAJOVÁ, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, David BEDNÁŘ and Martin MAREK. Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2020, vol. 18, No 2020, p. 1497-1508. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2020.06.021.

KOKKONEN, Piia Pauliina, Michaela SLÁNSKÁ, Veronika DOČKALOVÁ, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Esther Maria MARQUEZ SANCHEZ - CARNERERO, Jiří DAMBORSKÝ, Petr KLÁN, Zbyněk PROKOP and David BEDNÁŘ. The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step. Computational and Structural Biotechnology Journal. Amsterdam: Elsevier, 2020, vol. 18, No 2020, p. 805-813. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2020.03.017.

DVOŘÁK, Petr, Pavel KREJČÍ, Lukáš BÁLEK, Lívia EISELLEOVÁ, Žaneta KONEČNÁ, Pavel DVOŘÁK, David BEDNÁŘ, Jan BREZOVSKÝ, Eva ŠEBESTOVÁ, Radka CHALOUPKOVÁ, Veronika ŠTĚPÁNKOVÁ, Pavel VAŇÁČEK, Zbyněk PROKOP, Jiří DAMBORSKÝ and Michaela BOSÁKOVÁ. Thermostable FGF2 Polypeptide, Use Thereof. 2020.

BYŠKA, Jan, Thomas TRAUTNER, Sérgio Manuel MARQUES, Jiří DAMBORSKÝ, Barbora KOZLÍKOVÁ and Manuela WALDNER. Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Computer Graphics Forum. Wiley-Blackwell, 2019, vol. 38, No 3, p. 441-453. ISSN 0167-7055. Available from: https://dx.doi.org/10.1111/cgf.13701.

KNOZ, Martin, Břetislav LIPOVÝ, Jakub HOLOUBEK, Jan ŽÍDEK, Johana BABRNÁKOVÁ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ, Vanessa HEARNDEN and Lucy VOJTOVÁ. Bilaminární kožní dermální náhrada: Vliv stabilního FGF2 na kapilární denzitu sledovanou pomocí modelů ex-ovo a in vivo. In Bioimplantologie 2019. 2019.

ŠTOURAČ, Jan, O. VAVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, Gabriela Filipa FONSECA PINTO, Andrea SCHENKMAYEROVÁ, Jiří DAMBORSKÝ and David BEDNÁŘ. Caver web: identification of tunnels and channels in proteins and analysis of ligand transport. In European Biotechnology Congress. 2019. ISSN 0168-1656. Available from: https://dx.doi.org/10.1016/j.jbiotec.2019.05.251.

ŠTOURAČ, Jan, Ondřej VÁVRA, Piia Pauliina KOKKONEN, Jiří FILIPOVIČ, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Jan BREZOVSKÝ, Jiří DAMBORSKÝ and David BEDNÁŘ. Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic acids research. Oxford: Oxford University Press, 2019, vol. 47, W1, p. 414-422. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz378.

VÁVRA, Ondřej, Jiří FILIPOVIČ, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Jan ŠTOURAČ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics. Oxford: Oxford University Press, 2019, vol. 35, No 23, p. 4986-4993. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btz386.

LIPOVÝ, Břetislav, Lucy VOJTOVÁ, Jakub HOLOUBEK, Jana ZÍDEK, Martin KNOZ, Johana BABRNAKOVA, Veronika PAVLIŇÁKOVÁ, Lucie VIŠTĚJNOVÁ, Veronika ŠTĚPÁNKOVÁ, Eva FILOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Vanessa HEARNDEN. Collagen-based dermal substitute with stable fibroblast growth factor 2 (FGF2): ex ovo and in vivo impact on neovascularization. In 12th Asia Pacific Burn Congress. 2019. ISSN 2321-3876. Available from: https://dx.doi.org/10.1186/s41038-019-0164-1.

MITCHELL, James, Fernanda BALEM, Kalyan TIRUPULA, David MAN, Harpreet Kaur DHIMAN, Naveena YANAMALA, Julian OLLESCH, Joan PLANAS IGLESIAS, Barbara J. JENNINGS, Klaus GERWERT, Alessandro IANNACCONE and Judith KLEIN-SEETHARAMAN. Comparison of the molecular properties of retinitis pigmentosa P23H and N15S amino acid replacements in rhodopsin. Plos one. San Francisco: Public Library of Science, 2019, vol. 14, No 5, p. 1-14. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0214639.

MUSIL, Miloš, Hannes KONEGGER, Jiří HON, David BEDNÁŘ and Jiří DAMBORSKÝ. Computational Design of Stable and Soluble Biocatalysts. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2019, vol. 9, No 2, p. 1033-1054. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.8b03613.

DEMKO, Martin, Lukáš CHRÁST, Pavel DVOŘÁK, Jiří DAMBORSKÝ and David ŠAFRÁNEK. Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms. Basel: MDPI, 2019, vol. 7, No 11, p. 553-581. ISSN 2076-2607. Available from: https://dx.doi.org/10.3390/microorganisms7110553.

MARQUES, Sérgio Manuel, David BEDNÁŘ and Jiří DAMBORSKÝ. Computational Study of Protein-Ligand Unbinding for Enzyme Engineering. FRONTIERS IN CHEMISTRY. LAUSANNE: FRONTIERS MEDIA SA, 2019, vol. 6, JAN 2019, p. 1-15. ISSN 2296-2646. Available from: https://dx.doi.org/10.3389/fchem.2018.00650.

BURYŠKA, Tomáš, Michal VAŠINA, Fabrice GIELEN, Pavel VAŇÁČEK, Liisa VAN VLIET, Jan JEZEK, Zdenek PILAT, Pavel ZEMÁNEK, Jiří DAMBORSKÝ, Florian HOLLFELDER and Zbyněk PROKOP. Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics. Analytical Chemistry. Washington, D.C.: AMER CHEMICAL SOC, 2019, vol. 91, No 15, p. 10008-10015. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.9b01839.

TRATSIAK, K., Tanyana PRUDNIKOVA, Ivana DRIENOVSKÁ, Jiří DAMBORSKÝ, Jiří BRYNDA, Petr PACHL, Michal KUTÝ, Radka CHALOUPKOVÁ, P. REZACOVA and I.K. SMATANOVA. Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS. CHESTER: INT UNION CRYSTALLOGRAPHY, 2019, vol. 75, MAY 2019, p. 324-331. ISSN 2053-230X. Available from: https://dx.doi.org/10.1107/S2053230X19002796.

PRUDNIKOVA, T., B. KASCAKOVA, J.R. MESTERS, P. GRINKEVICH, P. HAVLICKOVA, A. MAZUR, A. SHAPOSHNIKOVA, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, M. KUTY and I.K. SMATANOVA. Crystallization and Crystallographic Analysis of a Bradyrhizobium Elkanii USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site. CRYSTALS. BASEL: MDPI, 2019, vol. 9, No 7, p. 1-12. ISSN 2073-4352. Available from: https://dx.doi.org/10.3390/cryst9070375.

CHRÁST, Lukáš, K. TRATSIAK, Joan PLANAS IGLESIAS, Lukáš DANIEL, T. PRUDNIKOVA, Jan BREZOVSKÝ, David BEDNÁŘ, I.K. SMATANOVA, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17. Microorganisms. Basel: MDPI, 2019, vol. 7, No 11, p. 1-20. ISSN 2076-2607. Available from: https://dx.doi.org/10.3390/microorganisms7110498.

HOLOUBEK, Jakub, Břetislav LIPOVÝ, Martin KNOZ, Lucy VOJTOVÁ, Johana BABRNÁKOVÁ, Veronika PAVLINAKOVA, Lucie VISTEJNOVA, Veronika ŠTĚPÁNKOVÁ, Eva FILOVA, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Vanessa HEARNDEN. Development of an innovative nanostructured dermal matrix in combination with a hyperstable form of growth factor for fibroblasts (FGF2): Ex ovo and in vivo study. In 10th Congress of World Society for Reconstructive Microsurgery, Bologna, Italy. 2019.

NEVOLOVÁ, Šárka, Elisabet MAŇÁSKOVÁ, Stanislav MAZURENKO, Jiří DAMBORSKÝ and Zbyněk PROKOP. Development of Fluorescent Assay for Monitoring of Dehalogenase Activity. Biotechnology Journal. WEINHEIM: WILEY-V C H VERLAG GMBH, 2019, vol. 14, No 3, p. 1-6. ISSN 1860-6768. Available from: https://dx.doi.org/10.1002/biot.201800144.

KOKKONEN, Piia Pauliina, David BEDNÁŘ, G. PINTO, Zbyněk PROKOP and Jiří DAMBORSKÝ. Engineering enzyme access tunnels. BIOTECHNOLOGY ADVANCES. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD, 2019, vol. 37, No 6, p. 1-13. ISSN 0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2019.04.008.

JINDAL, Garima, Kateřina SLÁNSKÁ, Veselin KOLEV, Jiří DAMBORSKÝ, Zbyněk PROKOP and Arieh WARSHEL. Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase. Proceedings of the National Academy of Sciences of the United States of America. WASHINGTON: NATL ACAD SCIENCES, 2019, vol. 116, No 2, p. 389-394. ISSN 0027-8424. Available from: https://dx.doi.org/10.1073/pnas.1804979115.

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar, Ondřej VÁVRA, Jiří FILIPOVIČ, Jan ŠTOURAČ, David BEDNÁŘ and Jiří DAMBORSKÝ. Fast Screening of Inhibitor Binding/Unbinding using Novel Software Tool CaverDock. FRONTIERS IN CHEMISTRY. LAUSANNE: FRONTIERS MEDIA SA, 2019, vol. 7, OCT 29 2019, p. 1-14. ISSN 2296-2646. Available from: https://dx.doi.org/10.3389/fchem.2019.00709.

KOLEDOVÁ, Zuzana, Jakub SUMBAL, Anas RABATA, Gabin DE LA BOURDONNAYE, Radka CHALOUPKOVÁ, Barbara HRDLIČKOVÁ, Jiří DAMBORSKÝ and Veronika ŠTĚPÁNKOVÁ. Fibroblast Growth Factor 2 Protein Stability Provides Decreased Dependence on Heparin for Induction of FGFR Signaling and Alters ERK Signaling Dynamics. Frontiers in Cell and Developmental Biology. Lausanne: Frontiers Media S.A., 2019, vol. 7, No 331, p. 1-15. ISSN 2296-634X. Available from: https://dx.doi.org/10.3389/fcell.2019.00331.

HORVÁTH, Peter, Peter ŠEBEJ, David KOVÁŘ, Jiří DAMBORSKÝ, Zbyněk PROKOP and Petr KLÁN. Fluorescent pH Indicators for Neutral to Near-Alkaline Conditions Based on 9-Iminopyronin Derivatives. ACS Omega. WASHINGTON: American Chemical Society, 2019, vol. 4, No 3, p. 5479-5485. ISSN 2470-1343. Available from: https://dx.doi.org/10.1021/acsomega.9b00362.

SCHENKMAYEROVA, A., G. PINTO, Martin MAREK, Martin TOUL, Lenka HERNYCHOVÁ, Veronika LIŠKOVÁ, S. EMOND, David BEDNÁŘ, Zbyněk PROKOP, Radka CHALOUPKOVÁ, F. HOLLFELDER and U.T. BORNSCHEUER. Functional switching based on altered enzyme flexibility via InDel mutagenesis of a reconstructed ancestor. In European Biotechnology Congress. 2019. ISSN 0168-1656. Available from: https://dx.doi.org/10.1016/j.jbiotec.2019.05.118.

SVATOŇ, Roman, Zdeněk KALA, Vladimír PROCHÁZKA, Michal EID, Tomáš ANDRAŠINA, Karolina POREDSKÁ, Jana STRENKOVÁ, Radka CHALOUPKOVÁ and Lumír KUNOVSKÝ. Gastrointestinální stromální tumory rekta - hodnocení dat národního registru s ohledem na využití v klinické praxi (Gastrointestinal Stromal Tumours of the Rectum - Evaluating the National Registry Data with Respect to its Use in Clinical Practice). Klinická onkologie. Praha: Ambit Media, 2019, vol. 32, No 2, p. 117-123. ISSN 0862-495X. Available from: https://dx.doi.org/10.14735/amko2019117.

CHALOUPKOVÁ, Radka, Veronika LIŠKOVÁ, Martin TOUL, Klára MARKOVÁ, Eva ŠEBESTOVÁ, Lenka HERNYCHOVÁ, Martin MAREK, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Daniel PLUSKAL, Jitka WATERMAN, Zbyněk PROKOP and Jiří DAMBORSKÝ. Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts. ACS Catalysis. Washington, D.C.: AMER CHEMICAL SOC, 2019, vol. 9, No 6, p. 4810-4823. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.9b01031.

HOVÁDKOVÁ, Zuzana, Milos HRABOVSKÝ, Rostislav VÁŇA, Jakub POSPÍŠIL, Josef JAROŠ, Jiří DAMBORSKÝ, Kamil PARUCH and Aleš HAMPL. Nanopatterning Glass Surface For Localization Of Embryonic Stem Cells. In Microscopy Conference, 1-5.9.2019, Berlin, Germany. 2019.

LIPOVÝ, Břetislav, Lucy VOJTOVÁ, Jakub HOLOUBEK, Martin KNOZ, Jan ZÍDEK, Johana BABRŇAKOVA, Veronika PAVLIŇÁKOVÁ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Vanessa HEARNDEN. New collagen foam with nanotechnological modification as bi-layer dermal substitute: Influence of stable FGF2 on capillary density in different animal models. In The 8th International Conference on Biomedical Engineering and Biotechnology (ICBEB). 2019.

CERNY, J., P. BOZIKOVA, A. BALIK, Sérgio Manuel MARQUES and L. VYKLICKY. NMDA Receptor Opening and Closing-Transitions of a Molecular Machine Revealed by Molecular Dynamics. Biomolecules. BASEL: MDPI, 2019, vol. 9, No 10, p. 1-17. ISSN 2218-273X. Available from: https://dx.doi.org/10.3390/biom9100546.

LIPOVÝ, Břetislav, Lucy VOJTOVA, Veronika STEPANKOVA, Jakub HOLOUBEK, Martin KNOZ, Radka CHALOUPKOVÁ, Zdenek PAVLOVSKY, Martin FALDYNA, Eduard GOPFERT and Vanessa HEARNDEN. Stable fibroblast growth factors in burn medicine research. In Workshop of the European Club for Pediatric Burns. 2019.

MIČAN, Jan, Martin TOUL, David BEDNÁŘ and Jiří DAMBORSKÝ. Structural Biology and Protein Engineering of Thrombolytics. Computational and Structural Biology Journal. Amsterdam: Elsevier, 2019, vol. 17, No 2019, p. 917-938. ISSN 2001-0370. Available from: https://dx.doi.org/10.1016/j.csbj.2019.06.023.

KOKKONEN, Piia Pauliina, Táňa KOUDELÁKOVÁ, Radka CHALOUPKOVÁ, Lukáš DANIEL, Zbyněk PROKOP and Jiří DAMBORSKÝ. Structure-Function Relationships and Engineering of Haloalkane Dehalogenases. In Aerobic Utilization of Hydrocarbons, Oils, and Lipids. Cham: Springer, 2019, p. 367-387. 1. ISBN 978-3-319-50417-9. Available from: https://dx.doi.org/10.1007/978-3-319-50418-6_15.

PILAT, Zdenek, Jan JEZEK, Martin KIZOVSKY, Tereza KLEMENTOVA, Stanislav KRATKY, Jaroslav SOBOTA, Ota SAMEK, Pavel ZEMANEK, Tomáš BURYŠKA, Jiří DAMBORSKÝ and Zbyněk PROKOP. Surface-enhanced Raman Spectroscopy in Microfluidic Chips for Directed Evolution of Enzymes and Environmental Monitoring. In 2019 PHOTONICS & ELECTROMAGNETICS RESEARCH SYMPOSIUM - SPRING (PIERS-SPRING). New York: IEEE, 2019, p. 1301-1309. ISBN 978-1-7281-3403-1. Available from: https://dx.doi.org/10.1109/PIERS-Spring46901.2019.9017521.

KNOZ, Martin, Břetislav LIPOVÝ, Jakub HOLOUBEK, Zdeněk PAVLOVSKÝ, Johana BABRNÁKOVÁ, Veronika ŠTĚPÁNKOVÁ, Martin FALDYNA, Jiří DAMBORSKÝ and Lucy VOJTOVÁ. Testování bilaminární kožní náhrady obohacené stabilním FGF2 na ex ovo a in vivo modelech. In Mezioborové přístupy v hojení ran, Lednice na Moravě. 2019.

BEIER, Andy, Jiří DAMBORSKÝ and Zbyněk PROKOP. Transhalogenation Catalysed by Haloalkane Dehalogenases Engineered to Stop Natural Pathway at Intermediate. ADVANCED SYNTHESIS & CATALYSIS. WEINHEIM: WILEY-V C H VERLAG GMBH, 2019, vol. 361, No 11, p. 2438-2442. ISSN 1615-4150. Available from: https://dx.doi.org/10.1002/adsc.201900132.

JURČÍK, Adam, Katarína FURMANOVÁ, Jan BYŠKA, Vojtěch VONÁSEK, Ondřej VÁVRA, Pavol ULBRICH, Helwig HAUSER and Barbora KOZLÍKOVÁ. Visual Analysis of Ligand Trajectories in Molecular Dynamics. Online. In IEEE Pacific Visualization Symposium 2019. Bangkok, Thailand: IEEE, 2019, p. 212-221. ISBN 978-1-5386-9226-4. Available from: https://dx.doi.org/10.1109/PacificVis.2019.00032.

BURYŠKA, Tomáš, Petra BABKOVÁ, Ondřej VÁVRA, Jiří DAMBORSKÝ and Zbyněk PROKOP. A Haloalkane Dehalogenase From a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. American Society for Microbiology, 2018, vol. 84, No 2, p. 1-13. ISSN 0099-2240.

MAZURENKO, Stanislav, Jan ŠTOURAČ, Antonín KUNKA, S. NEDELJKOVIC, David BEDNÁŘ, Zbyněk PROKOP and Jiří DAMBORSKÝ. CalFitter: a web server for analysis of protein thermal denaturation data. Nucleic Acids Research. Oxford: Oxford University Press, 2018, vol. 46, W1, p. "W344"-"W349", 6 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gky358.

JURČÍK, Adam, David BEDNÁŘ, Jan BYŠKA, Sérgio Manuel MARQUES, Katarína FURMANOVÁ, Lukáš DANIEL, Piia Pauliina KOKKONEN, Jan BREZOVSKÝ, Ondřej STRNAD, Jan ŠTOURAČ, Antonín PAVELKA, Martin MANAK, Jiří DAMBORSKÝ and Barbora KOZLÍKOVÁ. CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics. 2018, vol. 34, No 20, p. 3586-3588. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/bty386.

BREZOVSKÝ, Jan, Barbora KOZLÍKOVÁ and Jiří DAMBORSKÝ. Computational Analysis of Protein Tunnels and Channels. In Bornscheuer U., Höhne M. Protein Engineering. Methods in Molecular Biology. New York, NY: Humana Press, 2018, p. 25-42. 1685. ISBN 978-1-4939-7364-4. Available from: https://dx.doi.org/10.1007/978-1-4939-7366-8_3.

MIČAN, Jan, David BEDNÁŘ and Jiří DAMBORSKÝ. Computational Enzyme Design of Haloalkane Dehalogenases for Yperite Degradation. In XV Discussions in Structural Molecular Biology. 2018. ISSN 1805-4382.

DVOŘÁK, Pavel, David BEDNÁŘ, Pavel VAŇÁČEK, Lukáš BÁLEK, Lívia EISELLEOVÁ, Veronika ŠTĚPÁNKOVÁ, Eva ŠEBESTOVÁ, Michaela BOSÁKOVÁ, Žaneta KONEČNÁ, Stanislav MAZURENKO, Antonín KUNKA, Tereza VÁŇOVÁ, Karolína ZOUFALOVÁ, Radka CHALOUPKOVÁ, Jan BREZOVSKÝ, Pavel KREJČÍ, Zbyněk PROKOP, Petr DVOŘÁK and Jiří DAMBORSKÝ. Computer-assisted engineering of hyperstable fibroblast growth factor 2. Biotechnology and Bioengineering. New York: Wiley, 2018, vol. 115, No 4, p. 850-862. ISSN 0006-3592. Available from: https://dx.doi.org/10.1002/bit.26531.

KOKKONEN, Piia Pauliina, David BEDNÁŘ, Veronika DOČKALOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site. Journal of Biological Chemistry. Bethesda, USA: Amer. Soc. Biochem. Mol. Biol., 2018, vol. 293, No 29, p. 11505-11512. ISSN 0021-9258. Available from: https://dx.doi.org/10.1074/jbc.RA117.000328.

PILAT, Z., M. KIZOVSKY, J. JEZEK, S. KRATKY, J. SOBOTA, Martin ŠILER, O. SAMEK, Tomáš BURYŠKA, Pavel VAŇÁČEK, Jiří DAMBORSKÝ, Zbyněk PROKOP and P. ZEMANEK. Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips. Sensors. Basel: MDPI AG, 2018, vol. 18, No 10, p. 1-18. ISSN 1424-8220. Available from: https://dx.doi.org/10.3390/s18103212.

KNOZ, Martin, Lucy VOJTOVÁ, Břetislav LIPOVÝ, Jakub HOLOUBEK, Johana BABRNÁKOVÁ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GOPFERT, Jiří DAMBORSKÝ and Hearnden VANESSA. Development of stable FGF2 enriched biopolymer nanostructured dermal substitute: Ex ovo and in vivo study. In 10th Anniversary of the European Plastic Surgery Research Council, August 23–25, 2018 Hamburg/Germany. 2018.

CHRÁST, Lukáš, Pavel DVOŘÁK, Radka CHALOUPKOVÁ, V. DE LORENZO and Jiří DAMBORSKÝ. Engineering of bacterial strains for degradation of environmental pollutants by synthetic biology. In The 43rd FEBS Congress. 2018. ISSN 2211-5463.

PROKOP, Zbyněk, A. GHOSE, Piia Pauliina KOKKONEN, J. SYKORA, David BEDNÁŘ, M. AMARO, Šárka NEVOLOVÁ, M. HOF and Jiří DAMBORSKÝ. Engineering of enzyme gating driven by molecular dynamics, transient kinetics, and single molecule spectroscopy. In The 43rd FEBS Congress. 2018. ISSN 2211-5463.

BEERENS, Koen, Stanislav MAZURENKO, Antonín KUNKA, Sérgio Manuel MARQUES, N. HANSEN, Miloš MUSIL, Radka CHALOUPKOVÁ, Jitka WATERMAN, Jan BREZOVSKÝ, David BEDNÁŘ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2018, vol. 8, No 10, p. 9420-9428. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.8b01677.

VAŇÁČEK, Pavel, Eva ŠEBESTOVÁ, Petra BABKOVÁ, Šárka NEVOLOVÁ, Lukáš DANIEL, Pavel DVOŘÁK, Veronika ŠTĚPÁNKOVÁ, Radka CHALOUPKOVÁ, Jan BREZOVSKÝ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2018, vol. 8, No 3, p. 2402-2412, 21 pp. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.7b03523.

SUMBAL, Jakub, Tereza VRÁNOVÁ, Veronika ŠTĚPÁNKOVÁ, Jiří DAMBORSKÝ, Aleš HAMPL and Zuzana KOLEDOVÁ. FGF2 hypersignalling as a tool to study mammary epithelial branched pattern formation. In 8th Annual meeting on stem cells, DNA damage and apoptosis, Karlov, 31.1.-3.2.2018. 2018.

HOLOUBEK, Jakub, Břetislav LIPOVÝ, Eva NEDOMOVA, Filip RŮŽIČKA, Lukáš VACEK, Martin KNOZ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Lucy VOJTOVÁ. First in vitro preliminary results of newly developed temporary antibacterial biopolymer hydrogels with selected growth factors. In 19th Congress of the International society for burn injuries, New Delhi, India. 2018.

CHRÁST, Lukáš, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Gram-scale Production of Recombinant Microbial Enzymes in Shake Flasks. FEMS Microbiology Letters. Elsevier Science, 2018, vol. 365, No 2, p. 1-7. ISSN 0378-1097. Available from: https://dx.doi.org/10.1093/femsle/fnx265.

KUNKA, Antonín, Jiří DAMBORSKÝ and Zbyněk PROKOP. Haloalkane Dehalogenases From Marine Organisms. MARINE ENZYMES AND SPECIALIZED METABOLISM, PT B. SAN DIEGO: ELSEVIER ACADEMIC PRESS INC, 2018, vol. 605, No 1, p. 203-251. ISSN 0076-6879. Available from: https://dx.doi.org/10.1016/bs.mie.2018.03.005.

SUMBALOVÁ, Lenka, Jan ŠTOURAČ, Tomáš MARTÍNEK, David BEDNÁŘ and Jiří DAMBORSKÝ. HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. Nucleic Acids Research. Oxford: Oxford University Press, 2018, vol. 46, W1, p. "W356"-"W362", 7 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gky417.

KAUSHIK, Shubhangi, Sérgio Manuel MARQUES, Prashant Kumar KHIRSARIYA, Kamil PARUCH, Lenka LIBICHOVÁ, Jan BREZOVSKÝ, Zbyněk PROKOP, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Impact of the access tunnel engineering on catalysis is strictly ligand-specific. the FEBS Journal. 2018, 285/2018, No 8, p. 1456-1476. ISSN 1742-464X. Available from: https://dx.doi.org/10.1111/febs.14418.

LIPOVÝ, Břetislav, Lucy VOJTOVÁ, Jakub HOLOUBEK, Martin KNOZ, Johana BABRNÁKOVÁ, Veronika PAVLINAKOVA, Lucie VIŠTEJNOVÁ, Veronika ŠTĚPÁNKOVÁ, Eva FILOVA, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Vanessa HEARNDEN. Innovative collagen-based nanotechnologically modified dermal substitute containing stable fibroblast growth factor 2 (FGF2): first impression of in-vitro and in-vivo models. In 19th Congress of the International Society for Burn Injuries, New Delhi, India. 2018.

LIPOVÝ, Břetislav, Lucy VOJTOVÁ, Jakub HOLOUBEK, Martin KNOZ, Johana BABRŇÁKOVÁ, Veronika PAVLIŇÁKOVÁ, Lucie VIŠTEJNOVÁ, Veronika ŠTĚPÁNKOVÁ, Eva FILOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Vanessa HEARNDEN. Inovativní dermální kolagenová matrix s nanovlákennou vrstvou obohacená o stabilní růstový faktor pro fibroblasty 2 (FGF2): První zkušenosti na in vitro a in vivo modelech. In 8th Central European Burn Congress, Bratislava. 2018. ISBN 978-80-972285-6-9.

KOKKONEN, Piia Pauliina, J. SYKORA, Zbyněk PROKOP, A. GHOSE, David BEDNÁŘ, M. AMARO, Koen BEERENS, Šárka NEVOLOVÁ, Michaela SLÁNSKÁ, Jan BREZOVSKÝ, Jiří DAMBORSKÝ and M. HOF. Molecular Gating of an Engineered Enzyme Captured in Real Time. Journal of the American Chemical Society. Washington: American Chemical Society, 2018, vol. 140, No 51, p. 17999-18008. ISSN 0002-7863. Available from: https://dx.doi.org/10.1021/jacs.8b09848.

PILAT, Z., J. JEZEK, O. SAMEK, P. ZEMANEK, Tomáš BURYŠKA, Jiří DAMBORSKÝ and Zbyněk PROKOP. OPTOFLUIDIC TECHNIQUES FOR DIRECTED EVOLUTION OF ENZYMES. In 16th International Seminar of the Institute-of-Scientific-Instruments-The-Czech-Academy-of-Sciences. 2018. ISBN 978-80-87441-23-7.

HOLOUBEK, Jakub, Břetislav LIPOVÝ, eva NEDOMOVÁ, Filip RŮŽIČKA, Lukáš VACEK, Martin KNOZ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Lucy VOJTOVÁ. Preliminary in vitro results of a temporary antimicrobial biopolymer hydrogel optimalization for selected growth factors in partial-thickness skin defects (8th CENTRAL EUROPEAN BURN CONGRESS). 2018. ISBN 978-80-972285-6-9.

POSPÍŠIL, Jakub, Šárka BIDMANOVÁ, Zuzana HOVÁDKOVÁ, Miloš HRABOVSKÝ, Kamil PARUCH, Jiří DAMBORSKÝ, Aleš HAMPL and Josef JAROŠ. Preparation of nanostructured surfaces to influence hPSC behavior. In 8th Annual meeting on stem cells, DNA damage and apoptosis, Karlov, 31.1.-3.2.2018. 2018.

DAMBORSKÝ, Jiří, Fedor NIKULENKOV, Alexandra SISÁKOVÁ, Štěpán HAVEL, Lumír KREJČÍ, Benoit Jean-Pierre CARBAIN, Jan BREZOVSKÝ, Lukáš DANIEL and Kamil PARUCH. Pyrazolotriazines as inhibitors of nucleases. 2018.

DAMBORSKÝ, Jiří, Fedor NIKULENKOV, Alexandra SISÁKOVÁ, Štěpán HAVEL, Lumír KREJČÍ, Benoit, Jean-Pierre CARBAIN, Jan BREZOVSKÝ, Lukáš DANIEL and Kamil PARUCH. Pyrazolotriazines as inhibitors of nucleases. 2018.

MAZURENKO, Stanislav, Šárka NEVOLOVÁ, Markéta KOTLÁNOVÁ, Jiří DAMBORSKÝ and Zbyněk PROKOP. Sensitive operation of enzyme-based biodevices by advanced signal processing. Plos one. San Francisco: Public Library of Science, 2018, vol. 13, No 6, p. 1-16. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0198913.

PILAT, Z., M. KIZOVSKY, J. JEZEK, S. KRATKY, J. SOBOTA, M. SILER, O. SAMEK, Tomáš BURYŠKA, Pavel VAŇÁČEK, Jiří DAMBORSKÝ, Zbyněk PROKOP and Pavel ZEMANEK. Surface-enhanced Raman spectroscopy of chloroalkanes in microfluidic chips. Online. In Zemanek, P. 21ST CZECH-POLISH-SLOVAK OPTICAL CONFERENCE ON WAVE AND QUANTUM ASPECTS OF CONTEMPORARY OPTICS. BELLINGHAM: SPIE-INT SOC OPTICAL ENGINEERING, 2018, p. 1-7. ISBN 978-1-5106-2608-9. Available from: https://dx.doi.org/10.1117/12.2518393.

KNOZ, Martin, Lucy VOJTOVÁ, Břetislav LIPOVÝ, Jakub HOLOUBEK, Johana BABRNÁKOVÁ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Vanessa HEARNDEN. Vývoj biopolymerní nanostrukturované dermální náhrady: Ex ovo a in vivo studie. In Bioimplantologie 2018. 2018.

KNOZ, Martin, Lucy VOJTOVÁ, Břetislav LIPOVÝ, Jakub HOLOUBEK, Johana BABRNÁKOVÁ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Vanessa HEARNDEN. Vývoj biopolymerní nanostrukturované dermální náhrady: In vivo studie na prasečím modelu. In Supplementum ke Kongresu sekce mladých chirurgů České chirurgické společnosti ČLS JEP Seč 14. – 15. 6. 2018, Rozhledy v Chirurgii. 2018. ISSN 0035-9351.

KNOZ, Martin, Lucy VOJTOVÁ, Břetislav LIPOVÝ, Jakub HOLOUBEK, Johana BABRNÁKOVÁ, Lucie VIŠTEJNOVÁ, Veronika ŠTĚPÁNKOVÁ, Zdeněk PAVLOVSKÝ, Martin FALDYNA, Eduard GÖPFERT, Jiří DAMBORSKÝ and Vanessa HEARNDEN. Vývoj biopolymerní nanostrukturované dermální náhrady: In vivo studie na prasečím modelu. 2018.

BABKOVÁ, Petra, Eva ŠEBESTOVÁ, Jan BREZOVSKÝ, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity. CHEMBIOCHEM. 2017, vol. 18, No 14, p. 1448-1456. ISSN 1439-4227. Available from: https://dx.doi.org/10.1002/cbic.201700197.

DVOŘÁK, Pavel, Pablo Ivan NIKEL, Jiří DAMBORSKÝ and Victor DE LORENZO. Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology. BIOTECHNOLOGY ADVANCES. Oxford: PERGAMON-ELSEVIER SCIENCE LTD, 2017, vol. 35, No 7, p. 845-866. ISSN 0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2017.08.001.

MAZURENKO, Stanislav, Antonín KUNKA, Koen BEERENS, Christopher JOHNSON, Jiří DAMBORSKÝ and Zbyněk PROKOP. CalFitter 1.0. 2017.

MARQUES, Sérgio Manuel, Zuzana DUNAJOVÁ, Zbyněk PROKOP, Radka CHALOUPKOVÁ, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling. JOURNAL OF CHEMICAL INFORMATION AND MODELING. DC USA: AMER CHEMICAL SOC, 2017, vol. 57, No 8, p. 1970-1989. ISSN 1549-9596. Available from: https://dx.doi.org/10.1021/acs.jcim.7b00070.

FILIPOVIČ, Jiří, Ondřej VÁVRA, Jan PLHÁK, David BEDNÁŘ, Sérgio Manuel MARQUES, Jan BREZOVSKÝ, Luděk MATYSKA and Jiří DAMBORSKÝ. CaverDock 1.0. 2017.

BREZOVSKÝ, Jan, Barbora KOZLÍKOVÁ and Jiří DAMBORSKÝ. Computational Analysis of Protein Tunnels and Channels. In Editors: Bornscheuer, Uwe T., Höhne, Matthias. PROTEIN ENGINEERING. METHODS AND PROTOCOLS. New York: Springer, 2017, p. 25-42. ISBN 978-1-4939-7366-8.

LIŠKOVÁ, Veronika, Veronika ŠTĚPÁNKOVÁ, David BEDNÁŘ, Jan BREZOVSKÝ, Zbyněk PROKOP, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear beta-Haloalkanes: Open–Solvated versus Occluded–Desolvated Active Sites. Angewandte Chemie International Edition. WEINHEIM, GERMANY: WILEY-V C H VERLAG, 2017, vol. 56, No 17, p. 4719-4723. ISSN 1433-7851. Available from: https://dx.doi.org/10.1002/anie.201611193.

POSPÍŠIL, Jakub, Josef Vincenc OBOŇA, Miloš HRABOVSKÝ, Jarmila MLČOUŠKOVÁ, Kateřina KREJČÍ, Šárka BIDMANOVÁ, Kamil PARUCH, Jiří DAMBORSKÝ, Aleš HAMPL and Josef JAROŠ. Direct nanopatterning of biomolecules by electron beam lithography for studying of cellular interaction. In XVII. mezioborové setkání mladých biologů, biochemiků a chemiků, Milovy, 30.5.-1.6.2017. 2017.

SUMBAL, Jakub, Veronika ŠTĚPÁNKOVÁ, Jiří DAMBORSKÝ and Zuzana KOLEDOVÁ. Dissecting the roles of fibroblast growth factor (FGF) signalling in mammary branching morphogenesis using hyperstable FGF2 variants. In XVII. mezioborové setkání mladých biologů, biochemiků a chemiků, Milovy, 30.5.-1.6.2017. 2017.

MARQUES, Sérgio Manuel, Lukáš DANIEL, Tomáš BURYŠKA, Zbyněk PROKOP, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. Enzyme Tunnels and Gates As Relevant Targets in Drug Design. MEDICINAL RESEARCH REVIEWS. Hoboken, USA: WILEY, 2017, vol. 37, No 5, p. 1095-1139. ISSN 0198-6325. Available from: https://dx.doi.org/10.1002/med.21430.

MAZURENKO, Stanislav, Antonín KUNKA, Koen BEERENS, Christopher M. JOHNSON, Jiří DAMBORSKÝ and Zbyněk PROKOP. Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating. Scientific Reports. London: NATURE PUBLISHING GROUP, 2017, vol. 7, November, p. nestránkováno, 14 pp. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-017-16360-y.

SUMBAL, Jakub, Veronika ŠTĚPÁNKOVÁ, Jiří DAMBORSKÝ, Aleš HAMPL and Zuzana KOLEDOVÁ. Fibroblast growth factor (FGF) as a dynamic regulator of mammary gland branching morphogenesis. In The Biomania Student Scientific Meeting 2017, Brno, 3.10.2017. 2017.

SUMBAL, Jakub, Veronika ŠTĚPÁNKOVÁ, Jiří DAMBORSKÝ, Aleš HAMPL and Zuzana KOLEDOVÁ. Fibroblast growth factor (FGF) hypersignalling leads to hyperplasia of mammary epithelium through a stronger erk pathway activation. In XVIII. setkání biochemiků a molekulárních biologů, Brno, 14.-15.11.2017. 2017.

SUMBAL, Jakub, Veronika ŠTĚPÁNKOVÁ, Jiří DAMBORSKÝ, Aleš HAMPL and Zuzana KOLEDOVÁ. Fibroblastový růstový faktor jako dynamický regulátor morfogeneze mléčné žlázy. In 61. Studentská vědecká konference, Brno, 24.5.2017. 2017.

MUSIL, Miloš, Jan ŠTOURAČ, Jaroslav BENDL, Jan BREZOVSKÝ, Zbyněk PROKOP, Jaroslav ZENDULKA, Tomáš MARTÍNEK, David BEDNÁŘ and Jiří DAMBORSKÝ. FireProt: Web Server for Automated Design of Thermostable Proteins. Nucleic Acids Research. Oxford: Oxford University Press, 2017, vol. 45, W1, p. "W393"-"W399", 7 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkx285.

MUSIL, Miloš, Jan ŠTOURAČ, Jaroslav BENDL, Jan BREZOVSKÝ, Zbyněk PROKOP, J. ZENDULKA, Tomáš MARTÍNEK, David BEDNÁŘ and Jiří DAMBORSKÝ. FireProt 1.0. 2017.

SMATANOVA, Ivana Kuta, Iuliia IERMAK, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Haloalkane dehalogenases as a subject for crystallographic studies. In ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES. 2017. ISSN 2053-2733.

CHIU, Flora W. Y., David KOVÁŘ, Stavros STAVRAKIS, Simon BERGER, Andrew J. DEMELLO, Zbyněk PROKOP and Jiří DAMBORSKÝ. High-throughput screening of haloalkane dehalogenase libraries based on a pH- sensitive assay using droplet-based microfluidics. 2017.

HON, Jiří, David BEDNÁŘ, Tomáš MARTÍNEK and Jiří DAMBORSKÝ. HTS 1.0. 2017.

KAUSHIK, Shubhangi, Zbyněk PROKOP, Jiří DAMBORSKÝ and Radka CHALOUPKOVÁ. Kinetics of Binding of Fluorescent Ligands to Enzymes with Engineered Access Tunnels. FEBS Journal. Hoboken, NJ USA: WILEY-BLACKWELL, 2017, vol. 284, No 1, p. 134-148. ISSN 1742-464X. Available from: https://dx.doi.org/10.1111/febs.13957.

KOTÍK, Martin, Pavel VAŇÁČEK, Antonín KUNKA, Zbyněk PROKOP and Jiří DAMBORSKÝ. Metagenome-derived Haloalkane Dehalogenases with Novel Catalytic Properties. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY. New York: Springer, 2017, vol. 101, No 16, p. 6385-6397. ISSN 0175-7598. Available from: https://dx.doi.org/10.1007/s00253-017-8393-3.

MAZURENKO, Stanislav, Jiří DAMBORSKÝ and Zbyněk PROKOP. Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets. In Rocha M.,De Paz J.F.,Pinto T.,Fdez-Riverola. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics. Německo: Springer International Publishing, 2017, p. 9-17. ISBN 978-3-319-60816-7. Available from: https://dx.doi.org/10.1007/978-3-319-60816-7_2.

SCHWARTE, Andreas, Maika GENZ, Lilly SKALDEN, Alberto NOBILI, Clare VICKERS, Okke MELSE, Remko KUIPERS, Henk_jan JOOSTEN, Jan ŠTOURAČ, Jaroslav BENDL, Jon BLACK, Peter HAASE, Coos BAAKMAN, Jiří DAMBORSKÝ, Uwe BORNSCHEUER, Gert VRIEND and Hanka VENSELAAR. NewProt – a Protein Engineering Portal. PROTEIN ENGINEERING, DESIGN & SELECTION. Oxford: OXFORD UNIV PRESS, 2017, vol. 30, No 6, p. 441-447. ISSN 1741-0126. Available from: https://dx.doi.org/10.1093/protein/gzx024.

SCHWARTE, A., M. GENZ, L. SKALDEN, A. NOBILI, C. VICKERS, O. MELSE, R. KUIPERS, H. JOOSTEN, Jan ŠTOURAČ, Jaroslav BENDL, J. BLACK, P. HAASE, C. BAAKMAN, Jiří DAMBORSKÝ, Uwe BORNSCHEUER, G. VRIEND and H. VENSELAAR. NewProt 1.0. 2017.

HON, Jiří, Matej LEXA, Tomáš MARTÍNEK and Jaroslav ZENDULKA. pqsfinder: identification of potential quadruplex forming sequences. 2017. Available from: https://dx.doi.org/10.18129/B9.bioc.pqsfinder.

PARUCH, Kamil, Benoit, Jean-Pierre CARBAIN, Štěpán HAVEL, Jiří DAMBORSKÝ, Jan BREZOVSKÝ, Lukáš DANIEL, Alexandra SISÁKOVÁ, Fedor NIKULENKOV and Lumír KREJČÍ. Pyrazolotriazines as inhibitors of nucleases. 2017.

BEDNÁŘ, David, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme gamma-hexachlorocyclohexane dehydrochlorinase LinA01 carrying thermostabilizing mutations by energy-based approach. 2017.

BEDNÁŘ, David, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DhaA101 carrying thermostabilizing mutations by evolution-based approach. 2017.

BEDNÁŘ, David, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DhaA112 carrying thermostabilizing mutations by energy-based approach. 2017.

BEDNÁŘ, David, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DhaA115 carrying thermostabilizing mutations by combine approach. 2017.

KOTÍK, M., Pavel VAŇÁČEK, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase eHLD2. 2017.

KOTÍK, M., Pavel VAŇÁČEK, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase eHLD3. 2017.

BABKOVÁ, Petra, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase LinB116 carrying thermostabilizing mutations by FRESCO with removed disulphide bridge. 2017.

VAŇÁČEK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme halohydrin dehalogenase HheC01 carrying thermostabilizing mutations. 2017.

BEDNÁŘ, David, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme halohydrin dehalogenase HheC-DJ carrying thermostabilizing mutations. 2017.

VAŇÁČEK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme halohydrin dehalogenase HheC-LT01 carrying thermostabilizing mutations. 2017.

BEDNÁŘ, David, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant enzyme halohydrin dehalogenase HheC-LT02 carrying thermostabilizing mutations. 2017.

KOKKONEN, Piia Pauliina, Táňa KOUDELÁKOVÁ, Radka CHALOUPKOVÁ, Lukáš DANIEL, Zbyněk PROKOP and Jiří DAMBORSKÝ. Structure-function Relationships and Engineering of Haloalkane Dehalogenases. Online. In Rojo, Fernando. HANDBOOK OF HYDROCARBON AND LIPID MICROBIOLOGY SERIES. AEROBIC UTILIZATION OF HYDROCARBONS, OILS, AND LIPIDS. Heidelberg: Springer, Cham, 2017, p. 1-21. ISBN 978-3-319-50419-3. Available from: https://dx.doi.org/10.1007/978-3-319-39782-5.

VOJTOVÁ, Lucy, Martin KNOZ, Břetislav LIPOVÝ, Martin FALDYNA, Eduard GOPFERT, Veronika ŠTĚPÁNKOVÁ, Jakub HOLOUBEK, Veronika ŠVACHOVÁ, Johana BABRNÁKOVÁ, Zdeněk PAVLOVSKÝ, Eva PROSECKÁ, Martin PLENCNER, Eva FILOVÁ, Barbara KUBEŠOVÁ, Vanessa HEARNDEN and Jiří DAMBORSKÝ. Vliv růstových faktorů na biologickou aktivitu nanostrukturovaných vstřebatelných kožních náhrad: in-vitro a in-vivo experimentální studie. In IX.mezinárodní konference Bioimplantologie. 2017.

VAD, Viktor, Jan BYŠKA, Adam JURČÍK, Ivan VIOLA, Eduard M. GRÖLLER, Helwig HAUSER, Sérgio Manuel MARQUES, Jiří DAMBORSKÝ and Barbora KOZLÍKOVÁ. Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. Online. In S. Bruckner, A. Hennemuth, and B. Kainz. Eurographics Workshop on Visual Computing for Biology and Medicine. Bremen, Germany: Eurographics Workshop on Visual Computing for Biology and Medicine, 2017, p. 33-42. ISBN 978-3-03868-036-9.

NEHYBOVÁ, Tereza, Jan ŠMARDA, Lukáš DANIEL, Marek STIBOREK, Viktor KANICKÝ, Ivan SPASOJEVIČ, Jan PREISLER, Jiří DAMBORSKÝ and Petr BENEŠ. Wedelolactone Acts as Proteasome Inhibitor in Breast Cancer Cells. International Journal of Molecular Sciences. Basel: MDPI, 2017, vol. 18, No 4, p. nestránkováno, 14 pp. ISSN 1422-0067. Available from: https://dx.doi.org/10.3390/ijms18040729.

PAVELKA, Antonín, Eva ŠEBESTOVÁ, Barbora KOZLÍKOVÁ, Jan BREZOVSKÝ, Jiří SOCHOR and Jiří DAMBORSKÝ. CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. IEEE/ACM Transactions on Computational Biology and Bioinformatics. IEEE Computer Society, 2016, vol. 13, No 3, p. 505 - 517. ISSN 1545-5963. Available from: https://dx.doi.org/10.1109/TCBB.2015.2459680.

BIDMANOVÁ, Šárka, Zbyněk PROKOP, Jiří DAMBORSKÝ, A. DÜRKOP and O.S. WOLFBEIS. Device for Detection of Halogenated Hydrocarbons. 2016.

BURYŠKA, Tomáš, Lukáš DANIEL, Antonín KUNKA, Jan BREZOVSKÝ, Jiří DAMBORSKÝ and Zbyněk PROKOP. Discovery of Novel Haloalkane Dehalogenase Inhibitors. Applied and Environmental Microbiology. WASHINGTON, DC (USA): AMER SOC MICROBIOLOGY, 2016, vol. 82, No 6, p. 1958-1965. ISSN 0099-2240. Available from: https://dx.doi.org/10.1128/AEM.03916-15.

BREZOVSKÝ, Jan, Petra BABKOVÁ, Oksana DEGTJARIK, Andrea FOŘTOVÁ, Artur Wiktor GÓRA, L. IERMAK, Petra ŘEZÁČOVÁ, Pavel DVOŘÁK, Ivana KUTÁ-SMATANOVÁ, Zbyněk PROKOP, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Engineering a de Novo Transport Tunnel. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2016, vol. 6, No 11, p. 7597-7610. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/acscatal.6b02081.

BIDMANOVÁ, Šárka, M.S. STEINER, Martina STEPAN, Kamila VYMAZALOVA, M.A. GRUBER, A. DUERKOP, Jiří DAMBORSKÝ, Zbyněk PROKOP and O.S. WOLFBEIS. Enzyme Based Test Stripes for the Visual or Photographic Detection and Quantitation of Gaseous Sulfur Mustard. ANALYTICAL CHEMISTRY. 2016, vol. 88, No 11, p. 6044-6049. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/acs.analchem.6b01272.

BIDMANOVÁ, Šárka, Markéta KOTLÁNOVÁ, T. RATAJ, Jiří DAMBORSKÝ, Martina TRTILEK and Zbyněk PROKOP. Fluorescence-Based Biosensor for Monitoring of Environmental Pollutants: From Concept to Field Application. Biosensors & bioelectronics : the international journal for the professional involved with research, technology and applications of biosensors and related devices. Elsevier Science, 2016, vol. 84, October, p. 97-105. ISSN 0956-5663. Available from: https://dx.doi.org/10.1016/j.bios.2015.12.010.

BENDL, J., Jan ŠTOURAČ, Eva ŠEBESTOVÁ, Ondřej VÁVRA, Miloš MUSIL, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. HotSpot Wizard 2.0: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering. Nucleic Acids Research. Oxford University Press, 2016, vol. 44, W1, p. "W479"-"W487", 9 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkw416.

PROKOP, Zbyněk, Pavel VAŇÁČEK and Jiří DAMBORSKÝ. Mikrofluidní čip pro teplotní gradient (Microfluidic chip for temperature gradient). 2016.

HAMPL, Aleš, Jakub POSPÍŠIL, Jozef Vincenc OBOŇA, Vratislav KOŠŤÁL, Rostislav VÁŇA, Miloš HRABOVSKÝ, Šárka BIDMANOVÁ, Kamil PARUCH, Jarmila MLČOUŠKOVÁ, Kateřina KREJČÍ, Jiří DAMBORSKÝ and Josef JAROŠ. Nanostructured molecular lawn-powerful tool for studying cellular interactions. In XXV. Biochemický sjezd, Praha, 13.-16.9.2016. 2016. ISBN 978-80-270-0331-0.

JAROŠ, Josef, Jakub POSPÍŠIL, Rostislav VÁŇA, Miloš HRABOVSKÝ, Josef OBOŇA, Vratislav KOŠŤÁL, Šárka BIDMANOVÁ, Kamil PARUCH, Jarmila MLČOUŠKOVÁ, Kateřina KREJČÍ, Jiří DAMBORSKÝ and Aleš HAMPL. Nanostructured Surfaces for Studying the Cellular Interactions. In 12th International Congress of Cell Biology, Praha, 21.-25.7.2016. 2016.

POSPÍŠIL, Jakub, Josef Vincenc OBOŇA, Vratislav KOŠŤÁL, Jarmila MLČOUŠKOVÁ, Kateřina KREJČÍ, Šárka BIDMANOVÁ, Kamil PARUCH, Jiří DAMBORSKÝ, Aleš HAMPL and Josef JAROŠ. Nanostrukturování povrchů jako slibný nástroj pro studium buněčných interakcí kmenových buněk. In XVI. mezioborové setkání mladých biologů, biochemiků a chemiků, Milovy, 10.-12.5.2016. 2016.

BENDL, Jaroslav, Miloš MUSIL, Jan ŠTOURAČ, Jaroslav ZENDULKA, Jiří DAMBORSKÝ and Jan BREZOVSKÝ. PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. PLOS COMPUTATIONAL BIOLOGY 12: e100496. 2016, vol. 12, No 5, p. "nestrankovano", 18 pp. ISSN 1553-734X. Available from: https://dx.doi.org/10.1371/journal.pcbi.1004962.

MARQUES, Sérgio Manuel, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. Role of Tunnels and Gates in Enzymatic Catalysis. In Svendsen, A. UNDERSTANDING ENZYMES: FUNCTION, DESIGN, ENGINEERING, AND ANALYSIS. USA: Pan Stanford Publishing, 2016, p. 421-463. prvni 1. ISBN 978-981-4669-32-0.

KRAUSKOVÁ, Ľubica, Jitka PROCHÁZKOVÁ, Martina KLAŠKOVÁ, Lenka FILIPOVÁ, Radka CHALOUPKOVÁ, Stanislav MALÝ, Jiří DAMBORSKÝ and Dominik HEGER. Suppression of protein inactivation during freezing by minimizing pH changes using ionic cryoprotectants. International Journal of Pharmaceutics. 2016, vol. 509, 1-2, p. 41-49. ISSN 0378-5173. Available from: https://dx.doi.org/10.1016/j.ijpharm.2016.05.031.

KRUPKA, Michal, Josef MASEK, Lucia BARKOCZIOVA, Pavlina Turanek KNOTIGOVA, Pavel KULICH, Jana PLOCKOVA, Robert LUKAC, Eliska BARTHELDYOVA, Stepan KOUDELKA, Radka CHALOUPKOVÁ, Marek SEBELA, Daniel ZYKA, Ladislav DROZ, Roman EFFENBERG, Miroslav LEDVINA, Andrew D. MILLER, Jaroslav TURANEK and Milan RASKA. The Position of His-Tag in Recombinant OspC and Application of Various Adjuvants Affects the Intensity and Quality of Specific Antibody Response after Immunization of Experimental Mice. Plos one. San Francisco: Public Library of Science, 2016, vol. 11, No 2, p. "nestrankovano", 17 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0148497.

LIŠKOVÁ, Veronika, David BEDNÁŘ, T. PRUDNIKOVA, P. REZACOVA, Táňa KOUDELÁKOVÁ, Eva ŠEBESTOVÁ, I., KUTA- SMATANOVÁ, Jan BREZOVSKÝ, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Balancing the Stability-Activity Trade-off by Fine-Tuning Dehalogenase Access Tunnels. ChemCatChem. 2015, vol. 7, No 4, p. 648-659. ISSN 1867-3880. Available from: https://dx.doi.org/10.1002/cctc.201402792.

ŠTOURAČ, Jan, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. CaverWeb 0,2. 2015.

BIDMANOVÁ, Šárka, Zbyněk PROKOP and Jiří DAMBORSKÝ. Detekční proužky (Enzymatic Stripes). 2015.

ŠARMÍROVÁ, Klaudia, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. DsvA from Saccharomonospora viridis DSM 43017. 2015.

CHRÁST, Lukáš, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Enzyme haloalkane dehalogenase DmxA from Marinobacter sp. ELB17 purified to homogeneity. 2015.

DVOŘÁK, Pavel, Lukáš CHRÁST, Pablo Ivan NIKEL, Radek FEDR, Karel SOUČEK, Miroslava SEDLÁČKOVÁ, Radka CHALOUPKOVÁ, Víctor LORENZO DE, Zbyněk PROKOP and Jiří DAMBORSKÝ. Exacerbation of Substrate Toxicity by IPTG in Escherichia coli BL21(DE3) Carrying a Synthetic Metabolic Pathway. Microbial Cell Factories. London: BioMed Central, 2015, vol. 14, December, p. "nestrankovano", 15 pp. ISSN 1475-2859. Available from: https://dx.doi.org/10.1186/s12934-015-0393-3.

BEDNÁŘ, David, Koen BEERENS, Eva ŠEBESTOVÁ, Jaroslav BENDL, S. KHARE, Radka CHALOUPKOVÁ, Zbyněk PROKOP, Jan BREZOVSKÝ, D. BAKER and Jiří DAMBORSKÝ. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLOS COMPUTATIONAL BIOLOGY. 2015, vol. 11, No 11, p. "nestrankovano", 20 pp. ISSN 1553-734X. Available from: https://dx.doi.org/10.1371/journal.pcbi.1004556.

ŠTOURAČ, Jan, Jaroslav BENDL, Eva ŠEBESTOVÁ, Ondřej VÁVRA, Miloš MUSIL, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. HotSpot Wizard 2.0. 2015.

ŠTĚPÁNKOVÁ, Veronika, Jiří DAMBORSKÝ and Radka CHALOUPKOVÁ. Hydrolases in Non-Conventional Media: Implications for Industrial Biocatalysis. In Peter Grunwald. INDUSTRIAL BIOCATALYSIS. New York: Pan Stanford Publishing, 2015, p. 583-620. ISBN 978-981-4463-88-1.

BUCHTOVÁ, marcela, Radka CHALOUPKOVÁ, Malgorzata ZAKRZEWSKA, Iva VESELÁ, Petra CELÁ, Jana BARÁTHOVÁ, Iva GUDERNOVÁ, Renata ZAJICKOVA, Lukáš TRANTÍREK, Jorge MARTIN, Martin KOSTAS, Jacek OTLEWSKI, Jiří DAMBORSKÝ, Alois KOZUBÍK, Antoni WIEDLOCHA and Pavel KREJČÍ. Instability restricts signaling of multiple fibroblast growth factors. Cellular and Molecular Life Sciences. Basel: Springer, 2015, vol. 72, No 12, p. 2445-2459. ISSN 1420-682X. Available from: https://dx.doi.org/10.1007/s00018-015-1856-8.

GIELEN, Fabrice, Tomáš BURYŠKA, Liisa VAN VLIET, Maren BUTZ, Jiří DAMBORSKÝ, Zbyněk PROKOP and Florian HOLLFELDER. Interfacing Microwells with Nanoliter Compartments: A Sampler Generating High-Resolution Concentration Gradients for Quantitative Biochemical Analyses in Droplets. Analytical Chemistry. 2015, vol. 87, No 1, p. 624-632. ISSN 0003-2700. Available from: https://dx.doi.org/10.1021/ac503336g.

DANIEL, Lukáš, Tomáš BURYŠKA, Zbyněk PROKOP, Jiří DAMBORSKÝ and Jan BREZOVSKÝ. Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases using in Silico Screening. Journal of Chemical Information and Modeling. 2015, vol. 55, No 1, p. 54-62. ISSN 1549-9596. Available from: https://dx.doi.org/10.1021/ci500486y.

POSPÍŠIL, Jakub, Josef JAROŠ, Jozef Vincenc OBOŇA, Kateřina KREJČÍ, Jarmila MLČOUŠKOVÁ, Šárka BIDMANOVÁ, Vratislav KOŠŤÁL, Kamil PARUCH, Jiří DAMBORSKÝ and Aleš HAMPL. Nanostructured surfaces as a promising tool for studying the cellular interactions. In Creating Life in 3D. 2015.

POSPÍŠIL, Jakub, Josef OBOŇA, Vratislav KOŠŤAL, Šárka BIDMANOVÁ, Jiří DAMBORSKÝ, Kamil PARUCH, Aleš HAMPL and Josef JAROŠ. Nanostructured surfaces for studying the cellular interactions. In In Frontiers in material and life sciences: Creating life in 3D. 2015. 2015.

POSPÍŠIL, Jakub, Josef JAROŠ, Oboňa JOZEF VINCENC, Kateřina KREJČÍ, Jarmila MLČOUŠKOVÁ, Šárka BIDMANOVÁ, Vratislav KOŠŤÁL, Kamil PARUCH, Jiří DAMBORSKÝ and Aleš HAMPL. Nanostrukturovaný povrch pro studium mezibuněčných interakcí kmenových buněk (Nanostructured surface for studying intracellular interaction of stem cell). In 59. Studentská vědecká konference LF MU. 2015.

POSPÍŠIL, Jakub, Josef JAROŠ, Jozef Vincenc OBOŇA, Kateřina KREJČÍ, Jarmila MLČOUŠKOVÁ, Šárka BIDMANOVÁ, Vratislav KOŠŤÁL, Kamil PARUCH, Jiří DAMBORSKÝ and Aleš HAMPL. Novel approach for studying of cell interactions via nanostructured surfaces. In 7th Annual meeting on stem cells, DNA damage and apoptosis. 2015.

BENDL, Jaroslav, Miloš MUSIL, Jan ŠTOURAČ, Jaroslav ZENDULKA, Jiří DAMBORSKÝ and Jan BREZOVSKÝ. PredictSNP 2.0. 2015.

POSPÍŠIL, Jakub, Josef JAROŠ, Jozef Vincenc OBOŇA, Kateřina KREJČÍ, Jarmila MLČOUŠKOVÁ, Šárka BIDMANOVÁ, Vratislav KOŠŤÁL, Kamil PARUCH, Jiří DAMBORSKÝ and Aleš HAMPL. Preparation of nanostructured molecular lawn as tool for studying the cellular interactions. In The BIOMANIA STUDENT SCIENTIFIC MEETING, Brno. 2015.

BABKOVÁ, Petra, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant ancestral enzyme ancDbjA-DbeA NOD1. 2015.

BABKOVÁ, Petra, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant ancestral enzyme ancDbjA-DbeA NOD2. 2015.

BABKOVÁ, Petra, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant ancestral enzyme ancDbjA-DbeA NOD3. 2015.

BABKOVÁ, Petra, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant ancestral enzyme ancDbjA-DbeA NOD4. 2015.

BABKOVÁ, Petra, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant ancestral enzyme ancDbjA-DbeA NOD5. 2015.

BABKOVÁ, Petra, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant ancestral enzyme ancHLD-Rluc. 2015.

BABKOVÁ, Petra, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Recombinant ancestral enzyme ancLinB-DmbA. 2015.

AMARO, M., Jan BREZOVSKÝ, Silvia KOVÁČOVÁ, J. SYKORA, David BEDNÁŘ, Václav NĚMEC, Veronika LIŠKOVÁ, Nagendra Prasad KURUMBANG, Koen BEERENS, Radka CHALOUPKOVÁ, Kamil PARUCH, Martina HOF and Jiří DAMBORSKÝ. Site-specific Analysis of Protein Hydration Based on Unnatural Amino Acid Fluorescence. Journal of the American Chemical Society. 2015, vol. 137, No 15, p. 4988-4992. ISSN 0002-7863. Available from: https://dx.doi.org/10.1021/jacs.5b01681.

GHUFRANA, S., Martina PAVLOVÁ, M.I. ARIF, C.P. POSTEMA, Jiří DAMBORSKÝ and D.B. JANSSEN. A Pseudomonas putida Strain Genetically Engineered for 1,2,3-Trichloropropane Bioremediation. Applied and Environmental Microbiology. 2014, vol. 80, No 17, p. 5467-5476. ISSN 0099-2240. Available from: https://dx.doi.org/10.1128/AEM.01620-14.

KOZLÍKOVÁ, Barbora, Eva ŠEBESTOVÁ, Vilém ŠUSTR, Jan BREZOVSKÝ, Ondřej STRNAD, Lukáš DANIEL, David BEDNÁŘ, Antonín PAVELKA, Martin MAŇÁK, Martin BEZDĚKA, Petr BENEŠ, Matúš KOTRY, Artur Wiktor GORA, Jiří DAMBORSKÝ and Jiří SOCHOR. Caver Analyst 1.0. 2014.

KOZLÍKOVÁ, Barbora, Eva ŠEBESTOVÁ, Vilém ŠUSTR, Jan BREZOVSKÝ, Ondřej STRNAD, Lukáš DANIEL, David BEDNÁŘ, Antonín PAVELKA, Martin MANAK, Martin BEZDĚKA, Petr BENEŠ, Matúš KOTRY, Artur Wiktor GORA, Jiří DAMBORSKÝ and Jiří SOCHOR. CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. Bioinformatics. Oxford University Press, 2014, vol. 30, No 18, p. 2684-2685. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btu364.

ŠTĚPÁNKOVÁ, Veronika, Pavel VAŇÁČEK, Jiří DAMBORSKÝ and Radka CHALOUPKOVÁ. Comparison of Catalysis by Haloalkane Dehalogenases in Aqueous Solutions of a Deep Eutectic and Organic Solvents. Green Chemistry. 2014, vol. 16, No 5, p. 2754-2761. ISSN 1463-9262. Available from: https://dx.doi.org/10.1039/c4gc00117f.

DAMBORSKÝ, Jiří and Jan BREZOVSKÝ. Computational Tools for Designing and Engineering Enzymes. Current Opinion in Chemical Biology. 2014, vol. 19, april, p. 8-16. ISSN 1367-5931.

ŠEBESTOVÁ, Eva, Jaroslav BENDL, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. Computational Tools for Designing Smart Libraries. In Gillam, E. M. J., Copp, J. N., Ackerley, D. F.,. Directed Evolution Library Creation. New York: Springer New York, 2014, p. 291-314. 2nd edition, 1197. ISBN 978-1-4939-1052-6. Available from: https://dx.doi.org/10.1007/978-1-4939-1053-3_20.

KURUMBANG, Nagendra Prasad, Pavel DVOŘÁK, Jaroslav BENDL, Jan BREZOVSKÝ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Computer-Assisted Engineering of Synthetic Pathway for Biodegradation of Toxic Persistent Pollutant. ACS Synthetic Biology. 2014, vol. 3, No 3, p. 172-181. ISSN 2161-5063. Available from: https://dx.doi.org/10.1021/sb400147n.

LAHODA, M., J.R. MESTERS, A. STSIAPANAVA, Radka CHALOUPKOVÁ, M. KUTY, Jiří DAMBORSKÝ and I. KUTA SMATANOVA. Crystallographic Analysis of 1,2,3–Trichloropropane Biodegradation by Haloalkane Dehalogenase DhaA31. Acta Crystallographica D. 2014, vol. 70, february, p. 209-217. ISSN 0907-4449. Available from: https://dx.doi.org/10.1107/S1399004713026254.

SYKORA, J., Jan BREZOVSKÝ, Táňa KOUDELÁKOVÁ, M. LAHODA, Andrea FOŘTOVÁ, T. CHERNOVETS, Radka CHALOUPKOVÁ, Veronika ŠTĚPÁNKOVÁ, Zbyněk PROKOP, I. KUTA SMATANOVA, M. HOF and Jiří DAMBORSKÝ. Dynamics and Hydration Explain Failed Functional Transformation in Dehalogenase Design. Nature Chemical Biology. 2014, vol. 10, No 6, p. 428-430. ISSN 1552-4450.

CHAVARRIA, M., G. DURANTE-RODRIGUEZ, T. KRELL, C. SANTIAGO, Jan BREZOVSKÝ, Jiří DAMBORSKÝ and V. DE LORENZO. Fructose 1-Phosphate is the One and Only Physiological Effector of the Cra (FruR) regulator of Pseudomonas putida. FEBS Open Bio. 2014, vol. 4, No 2014, p. 377-386. ISSN 2211-5463. Available from: https://dx.doi.org/10.1016/j.fob.2014.03.013.

DVOŘÁK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Geneticky modifikovaná bakterie degradující toxické environmentalní polutanty Ps. putida CF4 deg31 (Engineered bacterium degrading toxic environmental pollutant Ps. putida CF4 deg31 –glpR). 2014.

DVOŘÁK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Geneticky modifikovaná bakterie Pseudomonas putida CF4 deg 31 pro degradaci toxického environmentálního polutantu 1,2,3-trichlorpropanu na chromosomu (Engineered bacterium degrading toxic environmental pollutant Ps. putida CF4 deg31 chromosome). 2014.

DVOŘÁK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Geneticky modifikovaná bakterie Pseudomonas putida CF4 pro degradaci toxického environmentálního polutantu 1,2,3-trichlorpropanu na plasmidu. (Engineered bacterium degrading toxic environmental pollutant Ps. putida CF4 deg31 plasmid). 2014.

DVOŘÁK, Pavel, Šárka BIDMANOVÁ, Jiří DAMBORSKÝ and Zbyněk PROKOP. Immobilized Synthetic Pathway for Biodegradation of Toxic Recalcitrant Pollutant 1,2,3-Trichloropropane. Environmental Science & Technology. 2014, vol. 48, No 12, p. 6859-6866. ISSN 0013-936X. Available from: https://dx.doi.org/10.1021/es500396r.

DVOŘÁK, Pavel, Nagendra Prasad KURUMBANG, Jaroslav BENDL, Jan BREZOVSKÝ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Maximizing the Efficiency of Multi-enzyme Process by Stoichiometry Optimization. ChemBioChem. WEINHEIM: WILEY-VCH, 2014, vol. 15, No 13, p. 1891-1895. ISSN 1439-4227. Available from: https://dx.doi.org/10.1002/cbic.201402265.

BIDMANOVÁ, Šárka, Eva HRDLIČKOVÁ, Josef JAROŠ, Ladislav ILKOVICS, Aleš HAMPL, Jiří DAMBORSKÝ and Zbyněk PROKOP. Microscopic Monitoring Provides Information on Structure and Properties During Biocatalyst Immobilisation. Biotechnology Journal. WEINHEIM, GERMANY: WILEY-V C H VERLAG GMBH, 2014, vol. 9, No 6, p. 852-860. ISSN 1860-6768. Available from: https://dx.doi.org/10.1002/biot.201300049.

POSPÍŠIL, Jakub, Josef JAROŠ, Šárka BIDMANOVÁ, Kamil PARUCH, Jiří DAMBORSKÝ and Aleš HAMPL. Nanostructured surface modifications for stem cell studie. In 6th Annual meeting on stem cells, DNA damage and apoptosis, Modrava, 22.-24.10.2014. 2014.

BENDL, Jaroslav, Jan ŠTOURAČ, O. SALANDA, Antonín PAVELKA, E.D. WIEBEN, J. ZENDULKA, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations. PLOS Computational Biology. 2014, vol. 10, No 1, p. "nestrankovano", 11 pp. ISSN 1553-734X. Available from: https://dx.doi.org/10.1371/journal.pcbi.1003440.

VAŇÁČEK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Rekombinantní enzym haloalkane dehalogenase HTS001 (Recombinant enzyme haloalkane dehalogenase HTS001). 2014.

VAŇÁČEK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Rekombinantní enzym haloalkane dehalogenase HTS003 (Recombinant enzyme haloalkane dehalogenase HTS003). 2014.

VAŇÁČEK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Rekombinantní enzym haloalkane dehalogenase HTS004 (Recombinant enzyme haloalkane dehalogenase HTS004). 2014.

VAŇÁČEK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Rekombinantní enzym haloalkane dehalogenase HTS005 (Recombinant enzyme haloalkane dehalogenase HTS005). 2014.

VAŇÁČEK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Rekombinantní enzym haloalkane dehalogenase HTS006 (Recombinant enzyme haloalkane dehalogenase HTS006). 2014.

VAŇÁČEK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Rekombinantní enzym haloalkane dehalogenase HTS010 (Recombinant enzyme haloalkane dehalogenase HTS010). 2014.

VAŇÁČEK, Pavel, Zbyněk PROKOP and Jiří DAMBORSKÝ. Rekombinantní enzym haloalkane dehalogenase HTS013 (Recombinant enzyme haloalkane dehalogenase HTS013). 2014.

VYMETAL, Jiří, Sreenivas Reddy BATHULA, Jiří ČERNÝ, Radka CHALOUPKOVÁ, Lukáš ŽÍDEK, Vladimír SKLENÁŘ and Jiří VONDRÁŠEK. Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition. PROTEIN ENGINEERING DESIGN & SELECTION. OXFORD: OXFORD UNIV PRESS, 2014, vol. 27, No 12, p. 463-472. ISSN 1741-0126. Available from: https://dx.doi.org/10.1093/protein/gzu046.

MORIUCHI, Ryota, Hiroki TANAKA, Yuki NIKAWADORI, Mayuko ISHITSUKA, Michihiro ITO, Yoshiyuki OHTSUBO, Masataka TSUDA, Jiří DAMBORSKÝ, Zbyněk PROKOP and Yuji NAGATA. Stepwise Enhancement of Catalytic Performance of Haloalkane Dehalogenase LinB towards Beta-Hexachlorocyclohexane. Applied Microbiology and Biotechnology Express. London: Springer, 2014, vol. 4, No 72, p. 1-10. ISSN 2191-0855. Available from: https://dx.doi.org/10.1186/s13568-014-0072-5.

CHALOUPKOVÁ, Radka, T. PRUDNIKOVA, P. REZACOVA, Zbyněk PROKOP, Táňa KOUDELÁKOVÁ, Lukáš DANIEL, Jan BREZOVSKÝ, W. IKEDA-OHTSUBO, Y. SATO, M. KUTY, Y. NAGATA, I. KUTA SMATANOVA and Jiří DAMBORSKÝ. Structural and Functional Analysis of a Novel Haloalkane Dehalogenase with Two Halide-Binding Sites. Acta Crystallographica D. 2014, vol. 70, July, p. 1884-1897. ISSN 0907-4449. Available from: https://dx.doi.org/10.1107/S1399004714009018.

CHALOUPKOVÁ, Radka and Jiří DAMBORSKÝ. Upravený rekombinantní enzym haloalkan dehalogenasa DbeA 01 (Engineered recombinant enzyme haloalkane dehalogenase DbeA01). 2014.

CHALOUPKOVÁ, Radka and Jiří DAMBORSKÝ. Upravený rekombinantní enzym haloalkan dehalogenasa DbeA 02 (Engineered recombinant enzyme haloalkane dehalogenase DbeA02). 2014.

CHALOUPKOVÁ, Radka and Jiří DAMBORSKÝ. Upravený rekombinantní enzym haloalkan dehalogenase DbeA03 (Engineered recombinant enzyme haloalkane dehalogenase DbeA03). 2014.

AMARO, Mariana, Jan BREZOVSKÝ, Silvia KOVÁČOVÁ, Lukáš MAIER, Radka CHALOUPKOVÁ, Jan SYKORA, Kamil PARUCH, Jiří DAMBORSKÝ and Martin HOF. Are Time-Dependent Fluorescence Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore? Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2013, vol. 117, No 26, p. 7898-7906. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/jp403708c.

ŠTĚPÁNKOVÁ, Veronika, J. PATEROVA, Jiří DAMBORSKÝ, P. JUNGWIRTH, Radka CHALOUPKOVÁ and J. HEYDA. Cation-Specific Effects on Enzymatic Catalysis Driven by Interactions at the Tunnel Mouth. Journal of Physical Chemistry B. 2013, vol. 117, No 21, p. 6394-6402. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/jp401506v.

TRATSIAK, K., O. DEGTJARIK, I. DRIENOVSKA, Lukáš CHRÁST, P. REZACOVA, M. KUTY, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ and I. KUTA SMATANOVA. Crystallographic Analysis of New Psychrophilic Haloalkane Dehalogenases: DpcA from Psychrobacter cryohalolentis K5 and DmxA from Marinobacter sp. ELB17. Acta Crystallographica. 2013, vol. 2013, F69, p. 683-688. ISSN 1744-3091. Available from: https://dx.doi.org/10.1107/S1744309113012979.

DEGTJARIK, O., Radka CHALOUPKOVÁ, P. REZACOVA, M. KUTY, Jiří DAMBORSKÝ and I. KUTA SMATANOVA. Differences in crystallization of two LinB variants from Sphingobium japonicum UT26. Acta Crystallographica. 2013, vol. 69, Pt 3, p. 284-287. ISSN 1744-3091. Available from: https://dx.doi.org/10.1107/S1744309113002467.

FOŘTOVÁ, Andrea, Eva ŠEBESTOVÁ, Veronika ŠTĚPÁNKOVÁ, Táňa KOUDELÁKOVÁ, Lenka PÁLKOVÁ, Jiří DAMBORSKÝ and Radka CHALOUPKOVÁ. DspA from Strongylocentrotus purpuratus: the First Biochemically Characterized Haloalkane Dehalogenase of Non-Microbial Origin. Biochimie. Elsevier, 2013, vol. 95, No 11, p. 2091-2096. ISSN 0300-9084. Available from: https://dx.doi.org/10.1016/j.biochi.2013.07.025.

DVOŘÁK, Pavel, Jan BREZOVSKÝ, Zbyněk PROKOP and Jiří DAMBORSKÝ. E. coli degWT upravená bakterie degradující toxické environmentální polutanty. (Engineered bacterium degrading toxic environmental pollutant E. coli degWT). 2013.

DVOŘÁK, Pavel, Jan BREZOVSKÝ, Zbyněk PROKOP and Jiří DAMBORSKÝ. E. coli degWT-opt- upravená bakterie degradující toxické environmentální polutanty. (Engineered bacterium degrading toxic environmental pollutant E. coli degWT-opt). 2013.

DVOŘÁK, Pavel, Jan BREZOVSKÝ, Zbyněk PROKOP and Jiří DAMBORSKÝ. E. coli deg31 upravená bakterie degradující toxické environmentální polutanty. (Engineered bacterium degrading toxic environmental pollutant E. coli deg31). 2013.

DVOŘÁK, Pavel, Jan BREZOVSKÝ, Zbyněk PROKOP and Jiří DAMBORSKÝ. E. coli deg31-opt upravená bakterie degradující toxické environmentální polutanty. (Engineered bacterium degrading toxic environmental pollutant E. coli deg31-opt). 2013.

DVOŘÁK, Pavel, Jan BREZOVSKÝ, Zbyněk PROKOP and Jiří DAMBORSKÝ. E. coli deg90R upravená bakterie degradující toxické environmentální polutanty. (Engineered bacterium degrading toxic environmental pollutant E. coli deg90R). 2013.

DVOŘÁK, Pavel, Jan BREZOVSKÝ, Zbyněk PROKOP and Jiří DAMBORSKÝ. E. coli deg90R-opt upravená bakterie degradující toxické environmentální polutanty. (Engineered bacterium degrading toxic environmental pollutant E. coli deg90R-opt). 2013.

KOUDELÁKOVÁ, Táňa, Radka CHALOUPKOVÁ, Jan BREZOVSKÝ, Zbyněk PROKOP, Eva ŠEBESTOVÁ, M. HESSELER, M. KHABIRI, M. PLEVAKA, D. KULIK, I. KUTA SMATANOVA, P. REZACOVA, R. ETTRICH, U.T. BORNSCHEUER and Jiří DAMBORSKÝ. Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel. Angewandte Chemie International Edition. Verlag Chemie, 2013, vol. 52, No 7, p. 1959-1963. ISSN 1433-7851. Available from: https://dx.doi.org/10.1002/anie.201206708.

ŠTĚPÁNKOVÁ, Veronika, M. KHABIRI, Jan BREZOVSKÝ, Antonín PAVELKA, J. SYKORA, M. AMARO, B. MINOFAR, Zbyněk PROKOP, M. HOF, R. ETTRICH, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents. ChemBioChem. WEINHEIM: WILEY-VCH, 2013, vol. 14, No 7, p. 890-897. ISSN 1439-4227. Available from: https://dx.doi.org/10.1002/cbic.201200733.

GORA, Artur Wiktor, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. Gates of Enzymes. Chemical Reviews. 2013, vol. 113, No 8, p. 5871-5923. ISSN 0009-2665. Available from: https://dx.doi.org/10.1021/cr300384w.

KOUDELÁKOVÁ, Táňa, Šárka BIDMANOVÁ, Pavel DVOŘÁK, Antonín PAVELKA, Radka CHALOUPKOVÁ, Zbyněk PROKOP and Jiří DAMBORSKÝ. Haloalkane dehalogenases: Biotechnological applications. Biotechnology Journal. HOBOKEN: WILEY-BLACKWELL, 2013, vol. 8, No 1, p. 32-45, 15 pp. ISSN 1860-6768. Available from: https://dx.doi.org/10.1002/biot.201100486.

BIDMANOVÁ, Šárka, Jiří DAMBORSKÝ and Zbyněk PROKOP. Immobilization of Haloalkane Dehalogenase LinB from Sphingobium japonicum UT26 for Biotechnological Applications. Journal of Biocatalysis & Biotransformation. 2013, vol. 2, No 2, p. 1-7. ISSN 2324-9099.

KHABIRI, M., B. MINOFAR, Jan BREZOVSKÝ, Jiří DAMBORSKÝ and R. ETTRICH. Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface. Journal of Molecular Modeling. du bureau d'adresse, 2013, vol. 19, No 11, p. 4701-4711. ISSN 1610-2940. Available from: https://dx.doi.org/10.1007/s00894-012-1507-z.

NOVOTNÁ, Jitka, Jana OLSOVSKA, Petr NOVAK, Peter MOJZEŠ, Radka CHALOUPKOVÁ, Zdenek KAMENIK, Jaroslav SPIZEK, Eva KUTEJOVA, Markéta MAREČKOVÁ, Pavel TICHY, Jiří DAMBORSKÝ and Jiri JANATA. Lincomycin Biosynthesis Involves a Tyrosine Hydroxylating Heme Protein of an Unusual Enzyme Family. Plos One. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2013, vol. 8, No 12, p. "e79974-1"-"e79974-10", 10 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0079974.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, F. OPLUŠTIL, Andrea JESENSKÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases. 2013.

DAMBORSKÝ, Jiří, Zbyněk PROKOP, Táňa KOUDELÁKOVÁ, Veronika ŠTĚPÁNKOVÁ, Radka CHALOUPKOVÁ, Eva CHOVANCOVÁ, Jan BREZOVSKÝ and Artur Wiktor GORA. Method of Thermostabilization of a Protein And/or Stabilization Towards Organic Solvents. 2013.

BIDMANOVÁ, Šárka, Zbyněk PROKOP and Jiří DAMBORSKÝ. Miniaturizovaný příruční fluorimetr (Miniaturized portable fluorimeter). 2013.

NIHARIKA, Neha, Hana MOSKALÍKOVÁ, Jasvinder KAUR, Miroslava SEDLÁČKOVÁ, Aleš HAMPL, Jiří DAMBORSKÝ, Zbyněk PROKOP and Rup LAL. Novosphingobium barchaimii sp nov., isolated from hexachlorocyclohexane-contaminated soil. International Journal of Systematic and Evolutionary Microbiology. SOC GENERAL MICROBIOLOGY, 2013, vol. 63, Part 2, p. 667-672. ISSN 1466-5026. Available from: https://dx.doi.org/10.1099/ijs.0.039826-0.

ŠTĚPÁNKOVÁ, Veronika, Jiří DAMBORSKÝ and Radka CHALOUPKOVÁ. Organic Co-solvents Affect Activity, Stability and Enantioselectivity of Haloalkane Dehalogenases. Biotechnology Journal. 2013, vol. 8, No 6, p. 719-729. ISSN 1860-6768. Available from: https://dx.doi.org/10.1002/biot.201200378.

BENDL, Jaroslav, Jan ŠTOURAČ, O. SALANDA, Antonín PAVELKA, E.D. WIEBEN, J. ZENDULKA, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. PredictSNP 1.0 (PredictSNP1.0). 2013.

PROKOP, Zbyněk, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Rekombinantní enzym haloalkan dehalogenáza DatA. (Recombinant enzyme haloalkane dehalogenase DatA). 2013.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP and Jiří DAMBORSKÝ. Rekombinantní enzym haloalkan dehalogenáza DspA. (Recombinant enzyme haloalkane dehalogenase DspA.). 2013.

HLADILKOVA, J., Zbyněk PROKOP, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ and P. JUNGWIRTH. Release of Halide Ions from the Buried Active Site of the Haloalkane Dehalogenase LinB Revealed by Stopped-Flow Fluorescence Analysis and Free Energy Calculations. Journal of Physical Chemistry B. 2013, vol. 117, No 46, p. 14329–14335. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/jp409040u.

BREZOVSKÝ, Jan, Eva ŠEBESTOVÁ, Artur Wiktor GORA, Antonín PAVELKA, Lada BIEDERMANNOVÁ and Jiří DAMBORSKÝ. Software tools for identification, visualization and analysis of protein tunnels and channels. BIOTECHNOLOGY ADVANCES. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD, 2013, vol. 31, No 1, p. 38-49. ISSN 0734-9750. Available from: https://dx.doi.org/10.1016/j.biotechadv.2012.02.002.

KAUR, Jasvinder, Hana MOSKALÍKOVÁ, Neha NIHARIKA, Miroslava SEDLÁČKOVÁ, Aleš HAMPL, Jiří DAMBORSKÝ, Zbyněk PROKOP and Rup LAL. Sphingobium baderi sp nov., isolated from a hexachlorocyclohexane dump site. International Journal of Systematic and Evolutionary Microbiology. SOC GENERAL MICROBIOLOGY, 2013, vol. 63, Part 2, p. 673-678. ISSN 1466-5026. Available from: https://dx.doi.org/10.1099/ijs.0.039834-0.

NIHARIKA, Neha, Hana MOSKALÍKOVÁ, Jasvinder KAUR, Fazlurrahman KHAN, Miroslava SEDLÁČKOVÁ, Aleš HAMPL, Jiří DAMBORSKÝ, Zbyněk PROKOP and Rup LAL. Sphingobium czechense sp nov., isolated from a hexachlorocyclohexane dump site. International Journal of Systematic and Evolutionary Microbiology. SOC GENERAL MICROBIOLOGY, 2013, vol. 63, Part 2, p. 723-728. ISSN 1466-5026. Available from: https://dx.doi.org/10.1099/ijs.0.039396-0.

ŠTĚPÁNKOVÁ, Veronika, Šárka BIDMANOVÁ, Táňa KOUDELÁKOVÁ, Zbyněk PROKOP, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Strategies for Stabilization and Activation of Biocatalysts in Organic Solvents. ACS Catalysis. 2013, vol. 3, No 12, p. 2823-2836. ISSN 2155-5435. Available from: https://dx.doi.org/10.1021/cs400684x.

HASAN, Khomaini, Artur Wiktor GORA, Jan BREZOVSKÝ, Radka CHALOUPKOVÁ, Hana MOSKALÍKOVÁ, Andrea FOŘTOVÁ, Yuji NAGATA, Jiří DAMBORSKÝ and Zbyněk PROKOP. The Effect of a Unique Halide-Stabilising Residue on the Catalytic Properties of Haloalkane Dehalogenase DatA from Agrobacterium tumefaciens C58. FEBS Journal. Blackwell, 2013, vol. 280, No 13, p. 3149-3159. ISSN 1742-464X. Available from: https://dx.doi.org/10.1111/febs.12238.

BURGESS, Rebecca C., Marek ŠEBESTA, Alexandra SISÁKOVÁ, María Victoria MARINI PALOMEQUE, Michael LISBY, Jiří DAMBORSKÝ, Hannah KLEIN, Rodney ROTHSTEIN and Lumír KREJČÍ. The PCNA Interaction Protein Box Sequence in Rad54 Is an Integral Part of Its ATPase Domain and Is Required for Efficient DNA Repair and Recombination. Plos One. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2013, vol. 8, No 12, p. "e82630", 10 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0082630.

BIEDERMANNOVÁ, Lada, Zbyněk PROKOP, Artur Wiktor GORA, Eva CHOVANCOVÁ, Mihály KOVÁCS, Jiří DAMBORSKÝ and Rebecca C. WADE. A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB. The Journal of Biological Chemistry. USA, 2012, vol. 287, No 34, p. 29062-29074. ISSN 0021-9258. Available from: https://dx.doi.org/10.1074/jbc.M112.377853.

DRIENOVSKÁ, Ivana, Eva CHOVANCOVÁ, Táňa KOUDELÁKOVÁ, Jiří DAMBORSKÝ and Radka CHALOUPKOVÁ. Biochemical Characterization of a Novel Haloalkane Dehalogenase from a Cold-Adapted Bacterium. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 2012, vol. 78, No 14, p. 4995-4998. ISSN 0099-2240. Available from: https://dx.doi.org/10.1128/AEM.00485-12.

CHOVANCOVÁ, Eva, Antonín PAVELKA, Petr BENEŠ, Ondřej STRNAD, Jan BREZOVSKÝ, Barbora KOZLÍKOVÁ, Artur Wiktor GORA, Vilém ŠUSTR, Martin KLVAŇA, Petr MEDEK, Lada BIEDERMANNOVÁ, Jiří SOCHOR and Jiří DAMBORSKÝ. CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Computational Biology. 2012, vol. 8, No 10, p. "nestránkováno", 12 pp. ISSN 1553-7358. Available from: https://dx.doi.org/10.1371/journal.pcbi.1002708.

BIDMANOVÁ, Šárka, Antonín HLAVÁČEK, Jiří DAMBORSKÝ and Zbyněk PROKOP. Conjugation of 5(6)-carboxyfluorescein and 5(6)-carboxynaphthfluorescein with bovine serum albumin and their immobilization for optical pH sensing. SENSORS AND ACTUATORS B: CHEMICAL. 2012, vol. 161, No 1, p. 93-99. ISSN 0925-4005. Available from: https://dx.doi.org/10.1016/j.snb.2011.09.046.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Jiří DAMBORSKÝ and Táňa KOUDELÁKOVÁ. Engineered recombinant enzyme haloalkane dehalogenase DhaA57. 2012.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Jiří DAMBORSKÝ and Táňa KOUDELÁKOVÁ. Engineered recombinant enzyme haloalkane dehalogenase DhaA61. 2012.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Jiří DAMBORSKÝ and Táňa KOUDELÁKOVÁ. Engineered recombinant enzyme haloalkane dehalogenase DhaA63. 2012.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Jiří DAMBORSKÝ and Táňa KOUDELÁKOVÁ. Engineered recombinant enzyme haloalkane dehalogenase DhaA80. 2012.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Jiří DAMBORSKÝ and Táňa KOUDELÁKOVÁ. Engineered recombinant enzyme haloalkane dehalogenase DhaA82. 2012.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Jiří DAMBORSKÝ and Táňa KOUDELÁKOVÁ. Engineered recombinant enzyme haloalkane dehalogenase DhaA85. 2012.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Jiří DAMBORSKÝ and Táňa KOUDELÁKOVÁ. Engineered recombinant enzyme haloalkane dehalogenase DhaA88. 2012.

BALONOVÁ, Lucie, B.F. MANN, Lukáš ČERVENÝ, W.R.Jr ALLEY, Eva CHOVANCOVÁ, Anna-Lena FORSLUND, E.N. SOLOMONSSON, A. FORSBEG, Jiří DAMBORSKÝ, L.V. NOVOTNÝ, Lenka HENRYCHOVÁ and Jiří STULÍK. Characterization of Protein Glycosylation in Francisella tularensis subsp. holarctica. Molecular and Cellurar Proteomic. Bethesda: Amer Soc Biochem Biol, 2012, vol. 11, No 7, p. 1-12. ISSN 1535-9476. Available from: https://dx.doi.org/10.1074/mcp.M111.015016.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, F. OPLUŠTIL, Andrea JESENSKÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases. 2012.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, F. OPLUŠTIL, Andrea JESENSKÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases. 2012.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, Filip OPLUŠTIL, Andrea FOŘTOVÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases. 2012.

DOKLÁDAL, Ladislav, Michal OBOŘIL, Karel STEJSKAL, Zbyněk ZDRÁHAL, Nikola PTÁČKOVÁ, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Tomáš KAŠPAROVSKÝ, Jeandroz SYLVAIN, Markéta ŽĎÁRSKÁ and Jan LOCHMAN. Physiological and proteomic approaches to evaluate the role of sterol binding in elicitin-induced resistance. Journal of Experimental Botany. Oxford: OXFORD UNIV PRESS, 2012, vol. 63, No 5, p. 2203-2215. ISSN 0022-0957. Available from: https://dx.doi.org/10.1093/jxb/err427.

CHOVANCOVÁ, Eva, Jan BREZOVSKÝ, Roman PANTŮČEK and Jiří DAMBORSKÝ. Výuka bioinformatiky pro studenty biologických oborů na Masarykově univerzitě. Online. In Petr Čech, Vojtěch Spiwok, Daniel Svozil. ENBIK Národní bioinformatická konference. Sborník ENBIK2012. Praha: Vysoká škola chemicko-technologická v Praze, 2012, p. 36. ISBN 978-80-7080-818-4.

BALCAROVÁ, Zdeňka, Sylvie HOLUBOVÁ, Radka CHALOUPKOVÁ and Libuše TRNKOVÁ. A Study of Cytosine Oligonucleotides by Voltammetric and Spectral Methods. In Biopolymers: Structure and dynamics, A biophysical workshop. 2011. ISBN 978-80-263-0050-2.

STRUHÁROVÁ, Iva, Pavel BOUCHAL, Jiří JARKOVSKÝ, Kristýna HRAZDILOVÁ, Monika DVOŘÁKOVÁ, Lenka HERNYCHOVÁ, Jiří DAMBORSKÝ, Petr SOVA and Bořivoj VOJTĚŠEK. An induction of Retinol Binding Protein 4 by new platinum-based anticancer agent LA-12. In "2nd RECAMO joint meeting": Role of p53, MDM2, AGR2/3 and ubiquitin/chaperone system in tumour biology. 2011. ISBN 978-80-86793-20-7.

SEDLACEK, Jiri, Šárka BIDMANOVÁ, Zbyněk PROKOP, Jiří DAMBORSKÝ, Bretislav MIKEL and Jaromir HUBALEK. Analyzer for Fluorescent Biosensing Application. Online. In Franz, M Nicolics, J Pietrikova, A. 2011 34TH INTERNATIONAL SPRING SEMINAR ON ELECTRONICS TECHNOLOGY (ISSE 2011) - NEW TRENDS IN MICRO/NANOTECHNOLOGY. NEW YORK: IEEE, 2011, p. 600-603. ISBN 978-1-4577-2110-6. Available from: https://dx.doi.org/10.1109/ISSE.2011.6053958.

DAMBORSKÝ, Jiří, Pavel DVOŘÁK, Zbyněk PROKOP, Radka CHALOUPKOVÁ, Martina PAVLOVÁ, Martin KLVAŇA, Michal OTYEPKA, R .C. WADE, Z. NAGATA, Eva HRDLIČKOVÁ and R. STLOUKAL. Biodegradation of 1,2,3-Trichloropropane. In Recent Trends in Developing Bioremediation Strategies for Hexachlorocyclohexane (HCH) & Other Chlorinated Contaminants. 2011.

HASAN, Khomaini, Andrea FOŘTOVÁ, Táňa KOUDELÁKOVÁ, Radka CHALOUPKOVÁ, M. ISHITSUKA, Yuji NAGATA, Jiří DAMBORSKÝ and Zbyněk PROKOP. Biochemical Characteristics of the Novel Haloalkane Dehalogenase DatA Isolated from the Plant Pathogen Agrobacterium tumefaciens C58. Applied and Environmental Microbiology. 2011, vol. 77, No 5, p. 1881-1884. ISSN 0099-2240. Available from: https://dx.doi.org/10.1128/AEM.02109-10.

BIEDERMANNOVÁ, Lada, Zbyněk PROKOP, Radka CHALOUPKOVÁ, Pavel DVOŘÁK, Jiří DAMBORSKÝ and R. WAADE. Biology and Bioinformatics. 2011.

CHOVANCOVÁ, Eva, Antonín PAVELKA, Petr BENEŠ, Ondřej STRNAD, Jan BREZOVSKÝ, Barbora KOZLÍKOVÁ, Artur Wiktor GORA, Vilém ŠUSTR, Martin KLVAŇA, Petr MEDEK, Lada BIEDERMANNOVÁ, Jiří DAMBORSKÝ and Jiří SOCHOR. CAVER 3.0. 2011.

CHOVANCOVÁ, Eva, Petr BENEŠ, Antonín PAVELKA, Petr MEDEK, Jan BREZOVSKÝ, Barbora KOZLÍKOVÁ, Martin KLVAŇA, Vilém ŠUSTR, Lada BIEDERMANNOVÁ, Ondřej STRNAD, Artur Wiktor GORA, Jiří SOCHOR and Jiří DAMBORSKÝ. CAVER 3.0: A Tool For Efficient Analysis Of Tunnels In Dynamic Protein Structures. In 3Dsig 2011, Structural Bioinformatics and Computational Biophysics, Vienna. 2011.

KLÁNOVÁ, Jana, Luděk BLÁHA, Jiří DAMBORSKÝ, Petr KLÁN, Ladislav DUŠEK and Ivan HOLOUBEK. CETOCOEN project: From the Laboratory to the Field and Beyond. Online. In Jiří Hřebíček, Gerald Schimak, Ralf Denzer. 9th IFIP WG 5.11 International Symposium on Environmental Software Systems: Frameworks of eEnvironment, ISESS 2011. Heidelberg: Springer, 2011, p. 491-499. ISBN 978-3-642-22284-9. Available from: https://dx.doi.org/10.1007/978-3-642-22285-6_53.

GORA, Artur Wiktor, Jan BREZOVSKÝ and Jiří DAMBORSKÝ. Computer-Assisted Enzyme Engineering by Modification of Tunnels, Channels and Gates. In European Biotechnology Congress. 2011.

DAMBORSKÝ, Jiří, Pavel DVOŘÁK, Radka CHALOUPKOVÁ and Zbyněk PROKOP. Construction of pollutant-degrading bacteria by protein and metabolic engineering. 2011.

LAHODA, M., Radka CHALOUPKOVÁ, Alena STSIAPANAVA, Jiří DAMBORSKÝ and I. SMATANOVA-KUTA. Crystallization and Crystallographic Analysis of the Rhodococcus rhodochrous NCIMB 13064 DhaA Mutant DhaA31 and its Complex with 1,2,3-Trichloropropane. Acta Crystallographica F. 2011, vol. 67, No 67, p. 397-400. ISSN 1744-3091. Available from: https://dx.doi.org/10.1107/S1744309111001254.

STSIAPANAVA, Alena, Radka CHALOUPKOVÁ, Andrea FOŘTOVÁ, J. BRYNDA, M. S. WEISS, Jiří DAMBORSKÝ and I. KUTÁ-SMATANOVÁ. Crystallization and Preliminary Crystallographic Analysis of Rhodococcus rhodochrous Wild-type DhAa Protein and its Variant DhaA13 Complexed with Different Ligands. In IX. Discussions in Structural Molecular Biology and Bioinformatics. 2011.

STSIAPANAVA, Alena, Radka CHALOUPKOVÁ, Andrea FOŘTOVÁ, J. BRYNDA, M. S. WEISS, Jiří DAMBORSKÝ and Ivana KUTÁ-SMATANOVÁ. Crystallization and Preliminary X-ray Diffraction Analysis of the Wild-Type Haloalkane Dehalogenase DhaA and its Variant DhaA13 Complexed with Different Ligands. Acta Crystallographica F. 2011, vol. 67, No 67, p. 253-257. ISSN 1744-3091. Available from: https://dx.doi.org/10.1107/S1744309110051286.

LAHODA, Maryna, Radka CHALOUPKOVÁ, Alena STSIAPANAVA, Jeroen MESTERS, Jiří DAMBORSKÝ and Ivana SMATANOVA-KUTÁ. Crystallization and structural analysis of DhaA31 from Rhodococcus rhodochrous. In IX. Discussions in Structural Molecular Biology and Bioinformatics,. 2011.

DAMBORSKÝ, Jiří, Radka CHALOUPKOVÁ and Zbyněk PROKOP. Decontamination kit Yperzyme. 2011.

PRUDNIKOVA, Tanyana, Radka CHALOUPKOVÁ, Yukari SATO, Yuji NAGATA, O. DEGTJARIK, Michal KUTÝ, P. REZACOVA, Jiří DAMBORSKÝ and Smatanova I. KUTA-SMATANOVÁ. Development of a Crystallization Protocol for the DbeA1 Variant of Novel Haloalkane Dehalogenase from Bradyrhizobium elkani USDA94. Crystal Growth & Design. 2011, vol. 11, No 2, p. 516-519. ISSN 1528-7483. Available from: https://dx.doi.org/10.1021/cg1013363.

BREZOVSKÝ, Jan, Veronika ŠTĚPÁNKOVÁ, Morteza KHABIRI, Antonín PAVELKA, Radka CHALOUPKOVÁ, Rudiger ETTRICH and Jiří DAMBORSKÝ. Effects of Organic Co-Solvents on Enzyme Activity: In Silico Analysis. In 3Dsig 2011, Structural Bioinformatics and Computational Biophysics,. 2011.

PLEŠKOVÁ, Veronika, Tomáš KAŠPAROVSKÝ, Michal OBOŘIL, Nikola PTÁČKOVÁ, Radka CHALOUPKOVÁ, Ladislav DOKLÁDAL, Jiří DAMBORSKÝ and Jan LOCHMAN. Elicitine-membrane interaction is driven by a positive charge on the protein surface: Role of Lys13 residue in lipids loading and resistance induction. Plant Physiology and Biochemistry. Elsevier, 2011, vol. 49, No 3, p. 321-328. ISSN 0981-9428. Available from: https://dx.doi.org/10.1016/j.plaphy.2011.01.008.

DAMBORSKÝ, Jiří. Engineering Robust and Efficient Protein Catalysts. In Biotech 2011 & Swiss/Czech Symposium. 2011.

HUBÁLEK, Jaromír, Jiří SEDLÁČEK, Zbyněk PROKOP, Šárka BIDMANOVÁ and Jiří DAMBORSKÝ. Fluorimetr pro biosensorové měření (Fluorimetr for biosensing measurements). 2011.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, Eva HRDLIČKOVÁ and Pavel TRTÍLEK. HaloPen. 2011.

PAVELKA, Antonín, Eva CHOVANCOVÁ and Jiří DAMBORSKÝ. HOTSPOT WIZARD: WEB APPLICATION FOR PROTEIN ENGINEERING AND STRUCTURAL ANNOTATION. In 3Dsig 2011, Structural Bioinformatics and Computational Biophysics, Vienna,. 2011.

DVOŘÁK, Pavel, Zbyněk PROKOP, Jan BREZOVSKÝ, David BEDNÁŘ, Šárka BIDMANOVÁ and Jiří DAMBORSKÝ. In vitro protein and metabolic engineering of a biodegradation pathway. In Biotrans 2011. 2011.

DAMBORSKÝ, Jiří. Keyhole-Lock-Key Model of Enzymatic Catalysis. 2011.

CHALOUPKOVÁ, Radka. Medium and protein engineering for improvement of biocatalysis in non-conventional media. 2011.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, František OPLUŠTIL, Andrea FOŘTOVÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases. 2011.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, F. OPLUŠTIL, Andrea JESENSKÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases,. 2011.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, František OPLUŠTIL, Andrea JESENSKÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases,. 2011.

SATO, Yukari, Zbyněk PROKOP, Jan BREZOVSKÝ, Ryo NATSUME, Yuji NAGATA, Jiří DAMBORSKÝ and Toshiya SENDA. Molecular bases of enantioselectivity of haloalkane dehalogenase DbjA. In Annual Meeting of American Crystallographic Association, New Orleans, USA,. 2011.

ŠTĚPÁNKOVÁ, Veronika, Radka CHALOUPKOVÁ, M. KHABIRI, Jan BREZOVSKÝ, Zbyněk PROKOP, Rudiger ETTRICH and Jiří DAMBORSKÝ. Molecular mechanisms of the effects of organic solvents on activity of haloalkane dehalogenases. 2011.

ŠTĚPÁNKOVÁ, Veronika, Radka CHALOUPKOVÁ, Morteza KHABIRI, Jan BREZOVSKÝ, Zbyněk PROKOP, Rudiger ETTRICH and Jiří DAMBORSKÝ. Molekulární podstata působení organických rozpouštědel na strukturu a funkci haloalkandehalogenáz (Molecular mechanisms of the effects of organic solvents on activity of haloalkane dehalogenases). 2011.

DAMBORSKÝ, Jiří, Zbyněk PROKOP and Hana MOSKALÍKOVÁ. Novosphingobium barchaimii LL02 sp. nov. 2011.

DAMBORSKÝ, Jiří, Radka CHALOUPKOVÁ and Zbyněk PROKOP. Recombinant enzyme haloalkane dehalogenase DmxA. 2011.

DAMBORSKÝ, Jiří, Radka CHALOUPKOVÁ and Zbyněk PROKOP. Recombinant enzyme haloalkane dehalogenase DpcA. 2011.

DAMBORSKÝ, Jiří, Radka CHALOUPKOVÁ and Zbyněk PROKOP. Recombinant enzyme haloalkane dehalogenase Spur. 2011.

DAMBORSKÝ, Jiří, Zbyněk PROKOP and Hana MOSKALÍKOVÁ. Sphingobium baderi LL03 sp. nov. 2011.

DAMBORSKÝ, Jiří, Zbyněk PROKOP and Hana MOSKALÍKOVÁ. Sphingobium czechense LL01 sp. nov. 2011.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Yukari SATO, Yuji NAGATA and Jiří DAMBORSKÝ. Stereoselectivity and Conformational Stability of Haloalkane Dehalogenase DbjA from Bradyrhizobium japonicum USDA110: The Effect of pH and Temperature. FEBS Journal. 2011, vol. 278, No 15, p. 2728-2738. ISSN 1742-464X. Available from: https://dx.doi.org/10.1111/j.1742-4658.2011.08203.x.

KOUDELÁKOVÁ, Táňa, Eva CHOVANCOVÁ, Jan BREZOVSKÝ, Marta MONINCOVÁ, Andrea FOŘTOVÁ, Jiří JARKOVSKÝ and Jiří DAMBORSKÝ. Substrate Specificity of Haloalkane Dehalogenases. Biochemical Journal. 2011, vol. 435, No 435, p. 345-354. ISSN 0264-6021. Available from: https://dx.doi.org/10.1042/BJ20101405.

STRUHÁROVÁ, Iva, Pavel BOUCHAL, Jiří JARKOVSKÝ, Kristýna HRAZDILOVÁ, Monika DVOŘÁKOVÁ, Lenka HERNYCHOVÁ, Jiří DAMBORSKÝ, Petr SOVA and Bořivoj VOJTĚŠEK. The new platinum anticancer agent LA-12 induces Retinol Bionding Protein 4 in vivo. In 5th European Summer School in "Proteomics Basics". 2011.

BOUCHAL, Pavel, Jiří JARKOVSKÝ, Kristýna HRAZDILOVÁ, Monika DVOŘÁKOVÁ, Iva STRUHÁROVÁ, Lenka HERNYCHOVÁ, Jiří DAMBORSKÝ, Petr SOVA and Bořivoj VOJTĚŠEK. The new platinum-based anticancer agent LA-12 induces retinol binding protein 4 in vivo. Proteome Science. BioMed Central, 2011, vol. 9, No 68, p. "nestránkováno", 9 pp. ISSN 1477-5956. Available from: https://dx.doi.org/10.1186/1477-5956-9-68.

MALČÍKOVÁ, Jitka, Boris TICHÝ, Jiří DAMBORSKÝ, Jitka KABÁTHOVÁ, Martin TRBUŠEK, Jiří MAYER and Šárka POSPÍŠILOVÁ. Analysis of the DNA-binding activity of p53 mutants using functional protein microarrays and its relationship to transcriptional activation. Biological Chemistry. Berlin, DE: Walter de Gruyter&CO, 2010, vol. 391, 2/3, p. 197-205. ISSN 1431-6730.

MALČÍKOVÁ, Jitka, Martin TRBUŠEK, Jana ŠMARDOVÁ, Jiří DAMBORSKÝ, Petr KUGLÍK, Boris TICHÝ, Jiří MAYER and Šárka POSPÍŠILOVÁ. Analýza p53 mutací in vitro a in vivo. In Konference Sigma-Aldrich v Chemické listy 104(5). 2010. ISSN 0009-2770.

STSIAPANAVA, Alena, J. DOHNÁLEK, J. GAVIRA, Michal KUTÝ, Táňa KOUDELÁKOVÁ, Jiří DAMBORSKÝ and Ivana KUTÁ-SMATANOVÁ. Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels. ACTA CRYSTALLOGRAPHICA D. International Union of Crystallography, 2010, vol. 66, No 66, p. 962-969. ISSN 0907-4449.

MOZGA, Tomáš, T. PRUDNIKOVA, Radka CHALOUPKOVÁ, P. REZACOVA, Yukari SATO, Michal KUTÝ, Zbyněk PROKOP, Yuji NAGATA, Ivana KUTÁ-SMATANOVÁ and Jiří DAMBORSKÝ. Biochemical and structural characterization of novel haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94 possesing two halide binding sites. In 8th Discussion in Structural Molecular Biology and Bioinformatics. 2010.

BENEŠ, Petr, Barbora KOZLÍKOVÁ, Ondřej STRNAD, Vilém ŠUSTR, Eva CHOVANCOVÁ, Antonín PAVELKA, Jan BREZOVSKÝ, Tibor SZABÓ, Matúš ZAMBORSKÝ, Jiří SOCHOR, Jiří DAMBORSKÝ and Lada BIEDERMANNOVÁ. CAVER 2.1. 2010.

BIDMANOVÁ, Šárka, Zbyněk PROKOP, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. CONSTRUCTION AND CHARACTERIZATION OF FIBER-OPTIC BIOSENSOR BASED ON HALOALKANE DEHALOGENASE. In Europt(r)ode X. 2010.

STSIAPANAVA, A., Radka CHALOUPKOVÁ, Andrea FOŘTOVÁ, J.R. MESTERS, J. BRYNDA, Jiří DAMBORSKÝ and Ivana KUTÁ-SMATANOVÁ. Crystallization and preliminary X-ray analysis of DhaA wild type and DhaA13 proteins from Rhodococcus rhodochrous. In 8th Discussion in Structural Molecular Biology and Bioinformatics. 2010.

FILIPI, T., P. MAZURA, Radka DOPITOVÁ, Lubomír JANDA, Jiří DAMBORSKÝ, N. S. KIRAN and B. BRZOBOHATY. DESIGNING RECOMBINANT MAIZE beta-GLUCOSIDASE Zm-p60.1: DEVELOPMENT OF NOVEL ENZYMES MODULATING CYTOKININ METABOLISM. In Skarpa, P. MENDELNET 2010. BRNO: MENDEL UNIV BRNO, FAC AGRONOMY, 2010, p. 821-823. ISBN 978-80-7375-453-2.

BIDMANOVÁ, Šárka, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ and Zbyněk PROKOP. Development of an enzymatic fiber-optic biosensor for detection of halogenated hydrocarbons. Analytical and Bioanalytical Chemistry. Springer-Verlag, 2010, vol. 10, No 1007, p. 1891-1898. ISSN 1618-2642.

BIDMANOVÁ, Šárka, Michal POHANKA, J. CABAL, Zbyněk PROKOP and Jiří DAMBORSKÝ. Early Warning Biosensors for Detection of Chemical Warfare Agents. CHEMICKE LISTY. Česká republika, 2010, vol. 104, No 104, p. 302-308. ISSN 0009-2770.

ŠTĚPÁNKOVÁ, Veronika, Radka CHALOUPKOVÁ, Morteza KHABIRI, Minofar BABÁK, Zbyněk PROKOP, R. ETTRICH and Jiří DAMBORSKÝ. Effect of organic solvents on structure and function of haloalkane dehalogenases. In 8th Discussion in Structural Molecular Biology and Bioinformatics. 2010.

PROKOP, Zbyněk, Yukari SATO, Jan BREZOVSKÝ, Tomáš MOZGA, Radka CHALOUPKOVÁ, Táňa KOUDELÁKOVÁ, Petr JEŘÁBEK, Veronika ŠTĚPÁNKOVÁ, Ryo NATSUME, J.G.E LEEUWEN, D.B. JANSSEN, Jan FLORIAN, Yuji NAGATA, Toshiya SENDA and Jiří DAMBORSKÝ. Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering. In Trends in Enzymology. 2010.

PROKOP, Zbyněk, Yukari SATO, Jan BREZOVSKÝ, Tomáš MOZGA, Radka CHALOUPKOVÁ, Táňa KOUDELÁKOVÁ, Petr JEŘÁBEK, Veronika ŠTĚPÁNKOVÁ, Rio NATSUME, J.G.E. LEEWEN, D,B. JANSSEN, J. FLORIAN, Yuji NAGATA, T. SENDA and Jiří DAMBORSKÝ. Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering. Angewandte Chemie International Edition. Wiley-VCH Verlag GmbH & Co. KGaA, Weinhe, 2010, vol. 49, No 35, p. 6111-6115. ISSN 1433-7851.

PROKOP, Zbyněk, Andrea FOŘTOVÁ, Radka CHALOUPKOVÁ, Martina PAVLOVÁ, Eva CHOVANCOVÁ, Jan BREZOVSKÝ, Martin KLVAŇA, Táňa KOUDELÁKOVÁ, Tomáš MOZGA, Antonín PAVELKA, Pavel DVOŘÁK, Monika STRAKOVÁ and Jiří DAMBORSKÝ. Engineering of Biocatalysts by Modification of Access Tunnels. In Novel Enzymes. 2010.

DAMBORSKÝ, Jiří, Zbyněk PROKOP, Radka CHALOUPKOVÁ, Eva CHOVANCOVÁ, Táňa KOUDELÁKOVÁ, Jan BREZOVSKÝ, Veronika ŠTĚPÁNKOVÁ, Antonín PAVELKA and Pavel DVOŘÁK. Engineering of Enzymes by Modification of Access Tunnels. In GEM 2010. 2010.

HASAN, Khomaini, Táňa KOUDELÁKOVÁ, Andrea FOŘTOVÁ, Radka CHALOUPKOVÁ, Yuji NAGATA, Jiří DAMBORSKÝ and Zbyněk PROKOP. Haloalkane dehalogenase from Agrobacterium tumefaciens C58 with new halide-stabilising residues and unique kinetics. In Trends in Enzymology. 2010.

CHOVANCOVÁ, Eva, Antonín PAVELKA and Jiří DAMBORSKÝ. HOTSPOT WIZARD: NÁSTROJ PRO INŽENÝRSTVÍ ENZYMŮ (HOTSPOT WIZARD: TOOL FOR ENGINEERING OF ENZYMES). In Konferenece Sigma-Aldrich, Milovy. 2010.

ŠTĚPÁNKOVÁ, Veronika, Radka CHALOUPKOVÁ, Jan BREZOVSKÝ, Morteza KHABIRI, R. ETTRICH and Jiří DAMBORSKÝ. How do organic solvents affecthaloalkane dehalogenases of haloalkane dehalogenases? In XIV. Setkání biochemiků a molekulárních biologů. 2010.

DRIENOVSKÁ, Ivana, Andrea FOŘTOVÁ, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Characterization of novel haloalkane dehalogenase DhcA from extremophilic microorganism Hahella chejuensis KCTC 2396. In GEM 2010. 2010.

DVOŘÁK, Pavel, Martina PAVLOVÁ, Martin KLVAŇA, Jan BREZOVSKÝ, Radka CHALOUPKOVÁ, Ivana VOLFOVÁ and Jiří DAMBORSKÝ. Increasing activity of bacterial biocatalyst with toxic anthropogenic substrate using methods of protein engineering. In 25th International Symposium on Microscale Bioseparations,. 2010.

BIEDERMANNOVÁ, Lada, Zbyněk PROKOP, Radka CHALOUPKOVÁ, Pavel DVOŘÁK, Jiří DAMBORSKÝ and R. WADE. Investigation of Ligand Passage in Proteins Investigation of Ligand Passage in Proteins. In Computational Chemistry. 2010.

HASAN, Khomaini, Táňa KOUDELÁKOVÁ, Andrea FOŘTOVÁ, Radka CHALOUPKOVÁ, Yuji NAGATA, Jiří DAMBORSKÝ and Zbyněk PROKOP. Kinetics and enantioselectivity of haloalkane dehalogenase from Agrobacterium tumefaciens c58. In XIV. Setkání biochemiků a molekulárních biologů. 2010.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, F. OPLUŠTIL, Andrea JESENSKÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases. 2010.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, František OPLUŠTIL, Andrea FOŘTOVÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases. 2010.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, František OPLUŠTIL, Andrea FOŘTOVÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases. 2010.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, F. OPLUŠTIL, Andrea JESENSKÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases,. 2010.

BIDMANOVÁ, Šárka, Zbyněk PROKOP, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Optical biosensor based on haloalkane dehalogenase for detection of halogenated hydrocarbons in the environment. In Biosensors. 2010.

DAMBORSKÝ, Jiří. Protein Engineering of Biocatalysts. 2010.

VEJVODA, Vojtech, David KUBAC, Alzbeta DAVIDOVA, Ondrej KAPLAN, Miroslav SULC, Ondrej SVEDA, Radka CHALOUPKOVÁ and Ludmila MARTINKOVA. Purification and characterization of nitrilase from Fusarium solani IMI196840. Process Biochemistry. Oxford: ELSEVIER SCI LTD, 2010, vol. 45, No 7, p. 1115-1120. ISSN 1359-5113. Available from: https://dx.doi.org/10.1016/j.procbio.2010.03.033.

ALTMANNOVÁ, Veronika, Nadine ECKERT-BOULET, Milica ARNERIC, Peter KOLESÁR, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ, Patrick SUNG, Xiaolan ZHAO, Michael LISBY and Lumír KREJČÍ. Rad52 SUMOylation affects the efficiency of the DNA repair. Nucleic Acids Research. Oxford University Press, 2010, vol. 38, No 6, 9 pp. ISSN 0305-1048.

SÝKORA, J., Martin HOF, Andrea FOŘTOVÁ and Jiří DAMBORSKÝ. SENSING HYDRATION AND MOBILITY AT THE VICINITY OF THE ACTIVE SITE OF ENZYMES BY MEANS OF FLUORESCENCE SPECTROSCOPY. 2010.

LAHODA, M., A. STSIAPANAVA, J. MESTERS, Táňa KOUDELÁKOVÁ, Jiří DAMBORSKÝ and Ivana KUTÁ-SMATANOVÁ. Structural analysis of DhaA12 mutant of the haloalkane dehalogenase from Rhodococcus rhodochrous NCIMB 13064,. In International School of Crystallography. 2010.

DAMBORSKÝ, Jiří, Táňa KOUDELÁKOVÁ and Veronika ŠTĚPÁNKOVÁ. Structure and activity of haloalkane dehalogenases in organic co-solvents. In , Gordon Research Conference. 2010.

ŠTĚPÁNKOVÁ, Veronika, Radka CHALOUPKOVÁ, Morteza KHABIRI, Minofar BABAK, Zbyněk PROKOP, R. ETTRICH and Jiří DAMBORSKÝ. Struktura a funkce haloalkándehalogenas v organických rozpouštědlech (Structure and funczional of haloalkandehalogenases in the organics solvents.). 2010.

MARTINS DOS SANTOS, V.A.P. and Jiří DAMBORSKÝ. Systems biology at work. Current Opinion in Biotechnology. Elsevier, 2010, vol. 21, No 21, p. 498-501. ISSN 0958-1669.

DAMBORSKÝ, Jiří. .: Keyhole-Lock-Key Model: Engineering of Tunnels in Proteins with Buried Active Sites. In 13. Australian Chemistry Days. 2009.

DAMBORSKÝ, Jiří and Jan BREZOVSKÝ. Computational Tools for Designing and Engineering Biocatalysts. CURRENT OPINION IN BIOLOGICAL CHEMISTRY. England, 2009, vol. 1, No 13, p. 26-34. ISSN 1367-5931.

DAMBORSKÝ, Jiří and Jiří SOCHOR. Computer-Assisted Engineering of Biomolecules. 2009.

PRUDNIKOVA, T., Tomáš MOZGA, P. REZACOVA, Radka CHALOUPKOVÁ, Yukari SATO, Yuji NAGATA, Y. BRYNDA, Michal KUTÝ, Jiří DAMBORSKÝ and Ivana KUTÁ-SMATANOVÁ. Crystallization and Preliminary X-ray Analysis of a Novel Haloalkane Dehalogenase DbeA from Bradyrhizobium elkani USDA94. Acta crystallographica. Section F Structural biology and crystallization communications. 2009, F65, No 1, p. 353-356. ISSN 1744-3091.

PAVLOVÁ, Martina, Martin KLVAŇA, Radka CHALOUPKOVÁ, Pavel BANÁŠ, Michal OTYEPKA, Rebecca WADE, Yuji NAGATA and Jiří DAMBORSKÝ. Design and Evolution of Haloalkane Dehalogenase with Enhanced Conversion of 1,2,3-Trichloropropane by Modification of Access Tunnels. Nature Chemical Biology. Nature Chemical Biology, 2009, vol. 5, xx, p. 727-733. ISSN 1552-4450.

DAMBORSKÝ, Jiří. Editorial: Protein Design and Engineering for Biocatalysis. BIOTECHNOLOGY JOURNAL. 2009, vol. 2009, No 4, 2 pp. ISSN 1860-6768.

DAMBORSKÝ, Jiří. Engineering of tunnels in proteins with buried active sites. 2009.

PAVELKA, Antonín, Eva CHOVANCOVÁ and Jiří DAMBORSKÝ. HotSpot Wizard: a web server for protein engineering. 2009.

PAVELKA, Antonín, Eva CHOVANCOVÁ and Jiří DAMBORSKÝ. HotSpot Wizard: a Web Server for Identification of Hot Spots in Protein Engineering. NUCLEIC ACIDS RESEARCH. 2009, vol. 2009, No 37, p. 376-383. ISSN 0305-1048.

JESENSKÁ, Andrea, Marta MONINCOVÁ, Táňa KOUDELÁKOVÁ, Khomaini HASAN, Radka CHALOUPKOVÁ, Zbyněk PROKOP, Z. GEERLOF and Jiří DAMBORSKÝ. Characterization of Haloalkane Dehalogenases DrbA and DmbC: Representatives of Novel Subfamily. (Biochemical Characterization of Haloalkane Dehalogenases DrbA and DmbC: Representatives of Novel Subfamily.). Applied and Environmental Microbilogy. 2009, vol. 75, No 15, p. 5157-5160. ISSN 0099-2240.

MOZGA, Tomáš, Zbyněk PROKOP, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Chiral Aliphatic Hydroxy Compounds in Nature: a Review of Biological Functions and Practical Applications. Collection of Czechoslovak chemical communications. 2009, vol. 74, 7-8, 83 pp. ISSN 0010-0765.

ŽOURKOVÁ, Alexandra, Ivana PALČÍKOVÁ, Jiří DAMBORSKÝ, Miroslav ROBEŠ and Lucie PULKRÁBKOVÁ. Klinické výsledky testování aktivity CYP2D6 a jejich srovnání s počítačovým modelováním (Clinical outcomes of testing activity CYP2D6 and comparison with computer modelling). Psychiatrie, časopis pro moderní psychiatrii. Praha: Tigis, 2009, vol. 13, suppl.1, p. 15. ISSN 1211-7579.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, F. OPLUŠTIL, Andrea JESENSKÁ and J. NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases (Method of detoxication of yperite by using haloalkane dehalogenases,). 2009.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, František OPLUŠTIL, Andrea FOŘTOVÁ and Yuji NAGATA. Method of detoxication of yperite by using haloalkane dehalogenases. 2009.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, Yuji NAGATA and D. B. JANSSEN. Method of Production of Optically Active Hydrocarbons and Alcohols Using Hydrolytic Dehalogenation Catalysed by Haloalkane Dehalogenases. 2009.

FOŘTOVÁ, Andrea, J. SÝKORA, Agniezska OLZYNSKA, Jan BREZOVSKÝ, Zbyněk ZDRÁHAL, Jiří DAMBORSKÝ and Martin HOF. Nanosecond Time-Dependent Stokes Shift at the Tunnel Mouth of Haloalkane Dehalogenases. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 2009, vol. 0000, No 131, p. 494-501, 12 pp. ISSN 0002-7863.

MACEK, Pavel, Josef CHMELÍK, Ivana KŘÍŽOVÁ, Pavel KADEŘÁVEK, Petr PADRTA, Lukáš ŽÍDEK, Marcela WILDOVÁ, Romana HADRAVOVÁ, Radka CHALOUPKOVÁ, Iva PICHOVÁ, Tomáš RUML, Michaela RUMLOVÁ and Vladimír SKLENÁŘ. NMR Structure of the N-Terminal Domain of Capsid Protein from the Mason-Pfizer Monkey Virus. Journal of Molecular Biology. 2009, vol. 392, No 1, p. 100-114. ISSN 0022-2836.

KLVAŇA, Martin, Martina PAVLOVÁ, Táňa KOUDELÁKOVÁ, Radka CHALOUPKOVÁ, Pavel DVOŘÁK, Zbyněk PROKOP, A. STSIAPANAVA, Michal KUTÝ, Ivana KUTÁ-SMATANOVÁ, J. DOHNÁLEK, Petr KULHÁNEK, R. WADE and Jiří DAMBORSKÝ. Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. JOURNAL OF MOLECULAR BIOLOGY. 2009, vol. 2009, No 00, p. 0000-0000, 10 pp. ISSN 0022-2836.

KOUDELÁKOVÁ, Táňa, Eva CHOVANCOVÁ, Jan BREZOVSKÝ, Martina PAVLOVÁ, Marta MONINCOVÁ, Tomáš MOZGA, Andrea FOŘTOVÁ, Khomaini HASAN, Pavel DVOŘÁK, J. JARKOVSKÝ and Jiří DAMBORSKÝ. Quantitative Analyses of Substrate Specifity of Haloalkane Dehalogenase. 2009.

PROKOP, Zbyněk and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DbeA. 2009.

PROKOP, Zbyněk and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DmbC. 2009.

PROKOP, Zbyněk and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DrbA. 2009.

PAVLOVÁ, Martina, Martin KLVAŇA, Radka CHALOUPKOVÁ, Pavel BANÁŠ, Michal OTYEPKA, R. WADE, Yuji NAGATA and Jiří DAMBORSKÝ. Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate. NATURE CHEMICAL BIOLOGY. 2009, vol. 0000, No 5, p. 727-733, 8 pp. ISSN 1552-4450.

BIEDERMANNOVÁ, Lada, Jiří DAMBORSKÝ and Rebecca WADE. Role of tunnels in enzymes. In Methods of Molecular Simulation (MMS) Heidelberg. 2009.

FOŘTOVÁ, Andrea, J. SÝKORA, A. OLZYŃSKA, Jan BREZOVSKÝ, Zbyněk ZDRÁHAL, Martin HOF and Jiří DAMBORSKÝ. Studium dynamiky molekul vody v ústí tunelu haloalkándehalogenáz (Study of water molecule dynamics at the tunnel openings of haloalkane dehalogenase). 2009.

FOŘTOVÁ, Andrea, J. SÝKORA, Agniezska OLZYNSKA, Jan BREZOVSKÝ, Zbyněk ZDRÁHAL, Martin HOF and Jiří DAMBORSKÝ. Study of water molecule dynamics at the tunnel openings of haloalkane dehalogenase. 2009.

KAZDA, Jindrich, Ivo PAVLIK, J.O. FALKLINHAM III., Karel HRUSKA, Jiří DAMBORSKÝ and Andrea FOŘTOVÁ. The ecology of Mycobacteria: Impact on Animal´s and Human Health. In DAMBORSKÝ, Jiří and Andrea FOŘTOVÁ. The ecology of Mycobacteria: Impact on Animal´s and Human Health. Heidelberg: Springer, 2009, p. 10-20, 10 pp. 2008940658. ISBN 978-1-4020-9412-5.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, Yuji NAGATA and D. JANSSEN. Způsob výroby opticky aktivních halogenalkanů a alkoholů hydrolytickou dehalogenací katalyzovanou halogenalkandehalogenázami (Method of Production of Optically Active Hydrocarbons and Alcohols Using Hydrolytic Dehalogenation Catalysed by Haloalkane Dehalogenases.). 2009.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, Yuji NAGATA and Dick JANSSEN. Způsob výroby opticky aktivních halogenalkanů a alkoholů hydrolytickou dehalogenací katalyzovanou halogenalkandehalogenázami (Production method of optically active alcohols of halogenalkan and hydrolytic dehalogenation catalyzed by halogenalkandehalogenases). 2009.

KOUDELÁKOVÁ, Táňa, Eva CHOVANCOVÁ, Martina PAVLOVÁ, Marta MONINCOVÁ, Tomáš MOZGA, Andrea FOŘTOVÁ, Khomaini HASAN, Pavel DVOŘÁK, J. JARKOVSKÝ and Jiří DAMBORSKÝ. Analysis of Substrate Specificities of Wild-type Haloalkane Dehalogenases and their Mutants by Multivariate Statistics. 2008.

GROCHOVÁ, Diana, Jana VAŇKOVÁ, Jiří DAMBORSKÝ, Barbora RAVČUKOVÁ, Jan ŠMARDA, Bořivoj VOJTĚŠEK and Jana ŠMARDOVÁ. Analysis of transactivation capability and conformation of p53 temperature-dependent mutants and their reactivation by amifostine in yeast. Oncogene. USA: Nature Publishing Group, 2008, vol. 27, No 9, p. 1243-1252. ISSN 0950-9232.

MEDEK, Petr, Petr BENEŠ, Barbora KOZLÍKOVÁ, Eva CHOVANCOVÁ, Antonín PAVELKA, Tibor SZABÓ, Matúš ZAMBORSKÝ, Filip ANDRES, Martin KLVAŇA, Jan BREZOVSKÝ, Jiří SOCHOR and Jiří DAMBORSKÝ. CAVER 2.0. 2008.

MONINCOVÁ, Marta, Yukari SATO, Yuji NAGATA and Jiří DAMBORSKÝ. Comparison of Broad-Specificity Haloalkane Dehalogenases DbjA and DmbA Using Multivariate Statistical Approach. xxxx. 2008, vol. 00, No 00, p. 00-00, 10 pp.

STSIASPANAVA, A., Táňa KOUDELÁKOVÁ, M. LAPKOUSKI, Martina PAVLOVÁ, Jiří DAMBORSKÝ and Ivana KUTÁ-SMATANOVÁ. Crystallization and preliminary diffraction analysis of Rhodococcus rhodocrous NCIMB 13064 DhaA mutants. 2008.

STSIASPANAVA, A., Táňa KOUDELÁKOVÁ, M. LAPKOUSKI, Martina PAVLOVÁ, Jiří DAMBORSKÝ and Ivana KUTÁ-SMATANOVÁ. Crystals of DhaA Mutants from Rhodococcus rhodochrous NCIMB 13064 Diffracted to Ultrahigh Resolution: Crystallization and Preliminary Diffraction Analysis. Acta Crystallographica Section D: Biological Crystallography. 2008, F, No 64, p. 137-140. ISSN 1744-3091.

PROKOP, Zbyněk, František OPLUŠTIL and Jiří DAMBORSKÝ. Decontamination of chemical warfare agent sulphur mustard. 2008.

BIDMANOVÁ, Šárka, Zbyněk PROKOP, Radka CHALOUPKOVÁ, G. KUNCOVÁ, J. BOLYÓ and Jiří DAMBORSKÝ. Development of Enzyme Biosensors for Detection of Toxic Halogenated Compounds. 2008.

MIKELOVÁ, Radka, Zbyněk PROKOP, Karel STEJSKAL, Vojtěch ADAM, Miroslava BEKLOVÁ, Libuše TRNKOVÁ, Bohumila KULICHOVÁ, A. HORNA, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ and René KIZEK. Enzymatic reaction coupled with flow-injection analysis with charged aerosol, coulometric, or amperometric detection for estimation of contamination of the environment by pesticides. Chromatographia. 2008, vol. 67, No 01, p. 47-53. ISSN 0009-5893.

PROKOP, Zbyněk, Jiří DAMBORSKÝ and Thomas SCHEPER. Fluorescence spectrophotometer TUH-01. 2008.

DOPITOVÁ, Radka, Pavel MAZURA, Lubomír JANDA, Radka CHALOUPKOVÁ, Petr JEŘÁBEK, Jiří DAMBORSKÝ, Tomáš FILIPI, Nagavalli S. KIRAN and Břetislav BRZOBOHATÝ. Functional analysis of the aglycone - binding site of the maize beta-glucosidase Zm-p60.1. FEBS Journal. 2008, vol. 275, No 24, p. 6123-6135. ISSN 1742-464X.

FLODROVÁ, Eva, Jan JUŘICA, Antonín PAVELKA, Petr JAŠA, Barbora RAVČUKOVÁ, Jana HÁZOVÁ, Eva CHOVANCOVÁ, Jiří DAMBORSKÝ, Renata GAILLYOVÁ and Alexandra ŽOURKOVÁ. Genetický polymorfismus CYP2D6 u pacientů léčených Paroxetinem a modelování mutantních forem CYP2D6 (Genetic polymorphism of CYP2D6 gene in the patient treated with Paroxetine and modeling of CYP2D6mutant form). In 12. Celostátní konference DNA diagnostiky. 2008.

PAVELKA, Antonín, Eva CHOVANCOVÁ and Jiří DAMBORSKÝ. HotSpot Wizard: Web Server for Identification of Hot Spots for Mutagenesis Experiments. 2008.

PAVELKA, Antonín, Eva CHOVANCOVÁ and Jiří DAMBORSKÝ. HOTSPOT WIZARD 1.0. 2008.

HASAN, Khomaini, Marta MONINCOVÁ, Andrea JESENSKÁ, Radka CHALOUPKOVÁ, Táňa KOUDELÁKOVÁ and Zbyněk PROKOP. Characterization of Haloalkane Dehalogenase DmbC from Mycobacterium tubercul.sis H37Rv, (Characterization of Haloalkane Dehalogenase DmbC from Mycobacterium tuberculosis H37Rv.). 2008.

PROKOP, Zbyněk, Martina PAVLOVÁ, Táňa KOUDELÁKOVÁ, Martin KLVAŇA, Tomáš MOZGA, Radka CHALOUPKOVÁ and Jiří DAMBORSKÝ. Inženýrství stereoselektivity enzymů pro aplikace biokatalýzy (Engineering of Enzymes Stereoselectivity for aplication of biocatalyses.). 2008.

BREZOVSKÝ, Jan, Zbyněk PROKOP, Yukari SATO, J. FLORIÁN, Tomáš MOZGA, Radka CHALOUPKOVÁ, Táňa KOUDELÁKOVÁ, Petr JEŘÁBEK, Rio NATSUME, D.B. JANSSEN, Yuji NAGATA, T. SENDA and Jiří DAMBORSKÝ. Modulation of Enantioselectivity in Haloalkane Dehalogenase DbjA by Engineering of a Surface Loop. 2008.

KLVAŇA, Martin, Martina PAVLOVÁ, Táňa KOUDELÁKOVÁ, Radka CHALOUPKOVÁ, Radka CHALOUPKOVÁ, Alena STSIAPANAVA, Michal KUTÝ, Ivana KUTÁ-SMATANOVÁ, J. DOHNÁLEK, Petr KULHÁNEK, R.C. WADE and Jiří DAMBORSKÝ. Pathways and Mechanisms for Product Exit and Water Exchange in Engineered Haloalkane Dehalogenase DhaA Exploredusing Classical and Random Acceleration Molecular Dynamics Simulations. 2008.

HOLUB, Peter, Martina PAVLOVÁ, Martin KLVAŇA, Zbyněk PROKOP, Radka CHALOUPKOVÁ, Aaron OAKLEY, M. TSUDA, Yuji NAGATA and Jiří DAMBORSKÝ. Protein Engineering of Haloalkane Dehalogenases: Towards the Change of Reaction Mechanism. 2008.

BREZOVSKÝ, Jan, Marta MONINCOVÁ, Zbyněk PROKOP, Yukari SATO, T. SENDA, Yuji NAGATA, R.C. WADE and Jiří DAMBORSKÝ. Quantitative Comparison of Binding Sites within the Protein Family of Haloalkane Dehalogenases,. 2008.

PROKOP, Zbyněk and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DbjA. 2008.

PROKOP, Zbyněk and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DhaA. 2008.

PROKOP, Zbyněk and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DhmA. 2008.

PROKOP, Zbyněk and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DmbA. 2008.

PROKOP, Zbyněk and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase DmbB. 2008.

PROKOP, Zbyněk and Jiří DAMBORSKÝ. Recombinant enzyme haloalkane dehalogenase LinB. 2008.

OTYEPKA, Michal, Pavel BANÁŠ, A. MAGISTRATO, P. CARLONI and Jiří DAMBORSKÝ. Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods. Proteins: Structure, Function, and Bioinformatics. 2008, vol. 70, No 000, p. 707-717. ISSN 0887-3585.

DAMBORSKÝ, Jiří, Radka CHALOUPKOVÁ, Martina PAVLOVÁ, Eva CHOVANCOVÁ and Jan BREZOVSKÝ. Structure-Function Relationships and Engineering of Haloalkane Dehalogenases. In Handbook of Hydrocarbon and Lipid Microbiology. 1st ed. Heidelberg: Springer, 2008, p. 1081-1098. Handbooks, 1. ISBN 978-3-540-77584-3.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Tomáš MOZGA, Yukari SATO, Táňa KOUDELÁKOVÁ, D.B. JANSSEN, Yuji NAGATA, T. SENDA and Jiří DAMBORSKÝ. Thermodynamic Analysis of Enantioselectivity of Haloalkane Dehalogenase DbjA and its Variants DbjA and DbjA+H139A towards Brominated Esters and substituted Bromoalkanes. 2008.

CHOVANCOVÁ, Eva and Jiří DAMBORSKÝ. Biomolecular Diversity. 2007.

BREZOVSKÝ, Jan, Marta MONINCOVÁ, Zbyněk PROKOP, Yukari SATO, Yuji NAGATA, R.C. WADE and Jiří DAMBORSKÝ. Comparative Binding Energy Analysis of Haloalkane Dehalogenase from Bradyrhizobium japonicum USDA110. 2007.

BREZOVSKÝ, Jan, Marta MONINCOVÁ, Zbyněk PROKOP, Yukari SATO, Yuji NAGATA, R.C. WADE and Jiří DAMBORSKÝ. Comparative Binding Energy (COMBINE) Analysis of the Substrate Specificity of Haloalkane Dehalogenase from Bradyrhizobium japonicum USDA110. 2007.

SATO, Yukari, Rio NATSUME, M. TSUDA, Jiří DAMBORSKÝ, Yuji NAGATA and T. SENDA. Crystallization and Preliminary Crystallographic Analysis of a Haloalkane Dehalogenase DbjA from Bradyrhizobium japonicum USDA110. Acta Crystallographica Section F. 2007, vol. 63, No 4, p. 294-296. ISSN 1744-3091.

STIAPANAVA, A., Táňa KOUDELÁKOVÁ, Lucie GRODECKÁ, Jiří DAMBORSKÝ and Iva KUTÁ-SMATANOVÁ. Crystallization study of three mutant haloalkane dehalogenases derived from dehalogenase DhaA of Rhodococcus rhodochrous NCIMB 13064. 2007.

ITO, M., Zbyněk PROKOP, Martin KLVAŇA, Y. OTSUBO, M. TSUDA, Jiří DAMBORSKÝ and Yuji NAGATA. Degradation of Beta-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Hexachlorocyclohexane-Utilizing Bacterium Sphingobium sp. MI1205. ARCHIVES IN MICROBIOLOGY. 2007, vol. 188, No 4, p. 313-325. ISSN 0302-8933.

BIDMANOVÁ, Šárka, Zbyněk PROKOP, G. KUNCOVÁ, J. BOLYÓ and Jiří DAMBORSKÝ. Development of Enzymatic Biosensors for Detection of Halogenated Environmental Pollutants. 2007.

DAMBORSKÝ, Jiří, Zbyněk PROKOP, Radka CHALOUPKOVÁ, Veronika ŠTĚPÁNKOVÁ, M. OLŠANSKÁ and F. OPLUŠTIL. Enzymatic Detoxification of Sulfur Mustard by Haloalkane Dehalogenases. 2007.

CHOVANCOVÁ, Eva, J. KOSINSKI, Janusz BUJNICKI and Jiří DAMBORSKÝ. Evolution of Haloalkane Dehalogenase Protein Family. 2007.

SILBERSTEIN, Michael, Jiří DAMBORSKÝ and Sandor VAJDA. Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Biochemistry. 2007, vol. 46, No 32, p. 9239-9249, 10 pp. ISSN 1520-4995.

FOHLEROVÁ, Radka, Pavel MAZURA, Lubomír JANDA, Radka CHALOUPKOVÁ, Petr JEŘÁBEK, Jiří DAMBORSKÝ and Břetislav BRZOBOHATÝ. Functional analysis of aglycone-binding site of the maize beta-glucosidase Zm-p60.1. In IPGSA 19th Annual Meeting-Abstracts. 2007.

FOHLEROVÁ, Radka, Pavel MAZURA, Lubomír JANDA, Radka CHALOUPKOVÁ, Petr JEŘÁBEK, Jiří DAMBORSKÝ and Břetislav BRZOBOHATÝ. Funkční analýza aglykon-vazebného místa kukuřičné beta-glukozidázy Zm-p60.1 (Functional analysis of aglycone-binding site of the maize beta glucosidase Zm-p60.1). In Bulletin České společnosti experimentální biologie rostlin a Fyziologické sekce Slovenské botanické společnosti. Olomouc: Česká společnost experimentální biologie rostlin, 2007, p. 106-106, 143 pp. ISSN 1213-6670.

PROKOP, Zbyněk, Yukari SATO, Tomáš MOZGA, Petr JEŘÁBEK, Rio NATSUME, J. FLORIÁN, M. TSUDA, Yuji NAGATA, T. SENDA and Jiří DAMBORSKÝ. Haloalkane Dehalogenases Possess Two Different Structural Bases for Their Enantioselectivity. 2007.

VAŠÍČKOVÁ, Petra, Eva MACHÁČKOVÁ, Miroslava LUKEŠOVÁ, Jiří DAMBORSKÝ, Ondřej HORKÝ, Hana PAVLŮ, jitka KUKLOVÁ, Veronika KOSINOVÁ, Marie NAVRÁTILOVÁ and Lenka FORETOVÁ. High Occurrence of BRCA1 Intragenic Rearrangements in Hereditary Breast and Ovarian Cancer Syndrome in the Czech Republic. BMC MEDICAL GENETICS. 2007, vol. 8, No 32, p. 1-11, 10 pp. ISSN 1471-2350.

DAMBORSKÝ, Jiří, Martin PETŘEK, Pavel BANÁŠ and Michal OTYEPKA. Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles. BIOTECHNOLOGY JOURNAL. 2007, vol. 2, No 1, p. 62-67. ISSN 1860-6768.

DAMBORSKÝ, Jiří and Zbyněk PROKOP. Keyhole-Lock-Key Model of Enzymatic Catalysis: Engineering of Tunnels in Proteins with Buried Active Sites. 2007.

KŘÍŽKOVÁ, Soňa, Jan HRADECKÝ, V. ŠUPÁLKOVÁ, Zbyněk PROKOP, Libuše TRNKOVÁ and Jiří DAMBORSKÝ. LinB Enzyme for Detection of Chlorinated Pesticides- Suggestion Design of a New Biosensor. 2007.

DAMBORSKÝ, Jiří. Meeting Report: Protein Design and Evolution for Biocatalysis. BIOTECHNOLOGY JOURNAL. 2007, vol. 2, No 2, p. 176-179. ISSN 1860-6768.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, D.B. JANSSEN and Yuji NAGATA. Method of Production of Optically Active Hydrocarbons and Alcohols Using Hydrolytic Dehalogenation Catalysed by Haloalkane Dehalogenases. 2007.

DAMBORSKÝ, Jiří. New Trends in Protein Engineering and White Biotechnologie. 2007.

CHOVANCOVÁ, Eva, Jan KOSINSKI, Janusz M. BUJNICKI and Jiří DAMBORSKÝ. Phylogenetic Analysis of Haloalkane Dehalogenases. Proteins: Structure, Function, and Bioinformatics. 2007, vol. 67, No 2, p. 305-316. ISSN 0887-3585.

CHROUST, Karel, Martina PAVLOVÁ, Zbyněk PROKOP, Jan MENDEL, Kateřina BOŽKOVÁ, Zdeněk KUBÁT, Věra ZAJÍČKOVÁ and Jiří DAMBORSKÝ. Quantitative Structure-Activity Relationships for Toxicity and Genotoxicity of Halogenated Aliphatic Compounds: Wing Spot Test of Drosophila melanogaster. CHEMOSPHERE. 2007, vol. 67, No 1, p. 152-159. ISSN 0045-6535.

NEGRI, A., E. MARCO, Jiří DAMBORSKÝ and Frederico GAGO. Stepwise Dissection and Visualization of the Catalytic Mechanism of Haloalkane Dehalogenase LinB using Molecular Dynamics Simulations and Computer Graphics. JOURNAL OF MOLECULAR GRAPHICS AND MODELLING. 2007, vol. 26, No 3, p. 643-651. ISSN 1093-3263.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Monika STRAKOVÁ, Tomáš MOZGA and Jiří DAMBORSKÝ. Stereoselectivity and Conformational Stability of Haloalkane Dehalogenase DbjA from Bradyrhizobium japonicum USDA110: The effect of temperature and pH. 2007.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Monika STRAKOVÁ, Yukari SATO, Yuji NAGATA and Jiří DAMBORSKÝ. Stereoselektivita a konformační stabilita halogenalkan dehalogenázy DbjA z Bradyrhizobium japonicum USDA110, (Stereoselectivity and Conformational Stability of Haloalkane Dehalogenase DbjA from Bradyrhizobium japonicum USDA110: The Effect of pH and Temperature). 2007.

PAPEŽOVÁ, Kateřina, Tomáš NĚMEC, Radka CHALOUPKOVÁ and Zdeněk GLATZ. Study of substrate inhibition by electrophoretically mediated microanalysis in partially filled capillary. Journal of Chromatography A. Amsterdam: Elsevier, 2007, vol. 1150, 1-2, p. 327-331. ISSN 0021-9673.

PAVLOVÁ, Martina, Martin KLVAŇA, Andrea JESENSKÁ, Zbyněk PROKOP, Hana KONEČNÁ, Yukari SATO, M. TSUDA, Yuji NAGATA and Jiří DAMBORSKÝ. The Identification of Catalytic Pentad in the Haloalkane Dehalogenase DhmA from Mycobacterium avium N85: Reaction Mechanism and Molecular Evolution. Journal of Structural Biology. 2007, vol. 157, No 2, p. 384-392. ISSN 1047-8477.

JANDERKA, Pavel and Radka CHALOUPKOVÁ. Use of Mass Spectrometer for Solid Sample Analysis. In 8th Advanced Batteries and Accumulators, Book of extended abstracts. 1st ed. Brno: Brno Univ. of Technology, 2007, p. 264-267, 5 pp. ISBN 978-80-214-3424-0.

PROKOP, Zbyněk, Radka CHALOUPKOVÁ, Martina PAVLOVÁ, Marta MONINCOVÁ, Michal STROUHAL, V. VELEBNÝ and Jiří DAMBORSKÝ. Využití enzymů ve farmaceutických výrobách (Development of Enzymes in the Farmaceuticals Industry.). 2007.

CHALOUPKOVÁ, Radka. ward of the Rector of the Masaryk University. 2007.

MONINCOVÁ, Marta, Zbyněk PROKOP, Jitka VEVODOVÁ, Yuji NAGATA and Jiří DAMBORSKÝ. Weak Activity of Haloalkane Dehalogenase LinB with 1,2,3-Trichloropropane Revealed by X-ray Crystallography and Microcalorimetry. Applied and Environmental Microbiology. 2007, vol. 73, No 6, p. 2005-2008. ISSN 0099-2240.

KOUDELÁKOVÁ, Táňa, Zbyněk PROKOP, Yukari SATO, Marta MONINCOVÁ, Andrea JESENSKÁ, Lucie GRODECKÁ, T. SENDA, Yuji NAGATA and Jiří DAMBORSKÝ. Změna enantioselektivity a substrátové specifity haloalkan dehalogenázy proteinovým inženýrstvím (Change of Enantioselectivity and Substrate Specifity od Haloalkan Dehalogenases by Protein Engineering.). 2007.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, František OPLUŠTIL, Andrea FOŘTOVÁ and Yuji NAGATA. ZPŮSOB DETOXIKACE SULFIDICKÉHO YPERITU ÚČINKEM HALOGENALKANDEHALOGENÁZ (Method of Detoxification of Yperite by using Haloalkane Dehalogenases). 2007.

MIKELOVÁ, Radka, Zbyněk PROKOP, Jan HRADECKÝ, Libuše TRNKOVÁ, Vojtěch ADAM, Jiří DAMBORSKÝ and René KIZEK. A suggestion of enzymatic biosensor for determination of chlorinated pesticides. In 11th International conference on electroanalysis. první. Bordeaux: European Society for ElectroAnalytical Chemistry, 2006, p. 1-45, 300 pp.

HRADECKÝ, Jan, Radka MIKELOVÁ, Zbyněk PROKOP, Libuše TRNKOVÁ, Jiří DAMBORSKÝ, Vojtěch ADAM, Jitka PETRLOVÁ and René KIZEK. A suggestion of enzymatic biosensor for determination of chlorinated pesticides. 2006.

MIKELOVÁ, Radka, Jan HRADECKÝ, Libuše TRNKOVÁ, David POTĚŠIL, Zbyněk PROKOP, Jiří DAMBORSKÝ, Jaroslav HUBÁLEK, Vojtěch ADAM and René KIZEK. Analýza chlorovaných uhlovodíků s využitím stříbrné a uhlíkové pastové elektrody (Analysis of chlorinated hydrocarbons using silver and carbon paste electrodes). In XXVI. Moderní elektrochemické metody. První. Praha: Česká společnost chemická, 2006, p. 51-56, 154 pp. ISBN 80-86238-98-9.

MALČÍKOVÁ, J., Jiří DAMBORSKÝ, B. TICHÝ, Jana KOTAŠKOVÁ, M. TRBUŠEK, J. MAYER and Š. POSPÍŠILOVÁ. Application of Functional Protein Microarrays for Detection of p53 Mutant Activity. 2006.

MALČÍKOVÁ, Jitka, Jiří DAMBORSKÝ, Boris TICHÝ, Jana KOTAŠKOVÁ, Martin TRBUŠEK, Jiří MAYER and Šárka POSPÍŠILOVÁ. Application of functional protein microarrays for detection of p53 mutation activity. In Advances in microarray technology, Amsterdam, Holandsko. 2006.

DAMBORSKÝ, Jiří. Bioinformatics III. 2006.

PETŘEK, Martin, Michal OTYEPKA, Pavel BANÁŠ, Jaroslav KOČA and Jiří DAMBORSKÝ. CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities. BMC BIOINFORMATICS. 2006, vol. 7, No 7, p. 316-324. ISSN 1471-2105.

PAVLOVÁ, Martina, Andrea FOŘTOVÁ, Martin KLVAŇA, Pavel BANÁŠ, Michal OTYEPKA, Yuji NAGATA and Jiří DAMBORSKÝ. Computer-assisted Directed Evolution of Haloalkane Dehalogenase DhaA Towards Degradation of 1,2,3-Trichloropropane. 2006.

HRADECKÝ, Jan, Radka MIKELOVÁ, Zbyněk PROKOP, Libuše TRNKOVÁ, Jiří DAMBORSKÝ, Vojtěch ADAM, Jana PETRLOVÁ and René KIZEK. Development of biosensor for determination of chlorinated pesticides. 2006.

MIKELOVÁ, Radka, Zbyněk PROKOP, Jan HRADECKÝ, Libuše TRNKOVÁ, Vojtěch ADAM, Miroslava BEKLOVÁ, Jiří DAMBORSKÝ and René KIZEK. Development of Enzymatic Biosensor for Determination of Chlorinated Pesticides. 2006.

PROKOP, Zbyněk, Yukari SATO, Tomáš MOZGA, D.B. JANSSEN, Yuji NAGATA and Jiří DAMBORSKÝ. Discovery of Stereoselective Haloalkane Dehalogenases: New Tool for Asymmetric Syntheses. 2006.

MIKELOVÁ, Radka, Libuše TRNKOVÁ, Jan HRADECKÝ, Vojtěch ADAM and Jiří DAMBORSKÝ. Electrochemical determination of chlorides on surfaces of carbon electrodes. 2006.

MIKELOVÁ, Radka, Libuše TRNKOVÁ, Jan HRADECKÝ, Vojtěch ADAM, Zbyněk PROKOP, Jiří DAMBORSKÝ and René KIZEK. Elektrochemické stanovení chloridů na uhlíkových elektrodách (Electrochemical determination of chlorides on surfaces of carbon electrodes). In Sborník příspěvků VI. Pracovního setkání fyzikálních chemiků a elektrochemiků. Brno: Masarykova universita, 2006, p. 70-71, 125 pp. ISBN 80-210-3943-4.

KOUDELÁKOVÁ, Táňa, Zbyněk PROKOP, Marta MONINCOVÁ, Andrea JESENSKÁ, Lucie GRODECKÁ, Yukari SATO, Yuji NAGATA and Jiří DAMBORSKÝ. Engineering of enantioselective enzyme by cumulative mutagenesis. 2006.

KOUDELÁKOVÁ, Táňa, Yukari SATO, Zbyněk PROKOP, Marta MONINCOVÁ, Andrea JESENSKÁ, Yuji NAGATA and Jiří DAMBORSKÝ. Engineering of Enantioselective Haloalkane Dehalogenase by Cumulative Mutagenesis. 2006.

KOUDELÁKOVÁ, Táňa, Zbyněk PROKOP, Yukari SATO, Marta MONINCOVÁ, Andrea FOŘTOVÁ, Lucie GRODECKÁ, T. SENDA, Yuji NAGATA and Jiří DAMBORSKÝ. Engineering of Haloalkane Dehalogenase DhaA from Rhodococcus rhodochrous NCIMB 13064 Towards Higher Enantioselectivity. 2006.

PROKOP, Zbyněk, František OPLUŠTIL, J. DEFRANK and Jiří DAMBORSKÝ. Enzymes Fight Chemicals Weapons. Biotechnology Journal. 2006, vol. 1, No 12, p. 1370-1380. ISSN 1860-6768.

HRADECKÝ, Jan, Radka MIKELOVÁ, Zbyněk PROKOP, Libuše TRNKOVÁ, Jiří DAMBORSKÝ, Vojtěch ADAM, Jitka PETRLOVÁ and René KIZEK. Enzymový Biosenzor pro detekci chlorovaných pesticidů (A suggestion of Enzymatic Biosensor for determination of chlorinated pesticides). In Sborník příspěvků X. pracovního setkání biochemiků a molekulárních biologů. Brno: Masarykova Universita, 2006, p. 66-67. ISBN 0-00-000000-0.

NAKAMURA, Takashi, Marcel ZAMOCKY, Zbyněk ZDRÁHAL, Radka CHALOUPKOVA, Marta MONINCOVÁ, Zbyněk PROKOP, Yuji NAGATA and Jiří DAMBORSKÝ. Expression of Glycosylated Haloalkane Dehalogenase LinB in Pichia pastoris. PROTEIN EXPRESSION AND PURIFICATION. 2006, 1/2006, No 46, p. 85-91. ISSN 1046-5928.

NAKAMURA, T., Marcel ZÁMOCKÝ, Zbyněk ZDRÁHAL, Radka CHALOUPKOVÁ, Marta MONINCOVÁ, Zbyněk PROKOP, Yuji NAGATA and Jiří DAMBORSKÝ. Expression of Haloalkane Dehalogenase LinB in Pichia pastoris. 2006.

MONINCOVÁ, Marta, Andrea FOŘTOVÁ, Radka CHALOUPKOVÁ, Yukari SATO, Zbyněk PROKOP and Jiří DAMBORSKÝ. High-throughput characterization of enzymes from genomic and proteomic projects-multivariate statistical approach. In Materials Structure in Chemistry, Biology, Physics and Technology. 2006.

DAMBORSKÝ, Jiří, Martin PETŘEK, Pavel BANÁŠ and Michal OTYEPKA. Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles. Biotechnology Journal. 2006, 1/2006, No 1, p. 9999-10007. ISSN 1860-6768.

DAMBORSKÝ, Jiří. Keyhole-Lock-Key Model of Enzyme-Substrate Binding. 2006.

BANÁŠ, Pavel, Michal OTYEPKA, Jitka VÉVODOVÁ, Petr JEŘÁBEK, Michal BOHÁČ, Martin PETŘEK and Jiří DAMBORSKÝ. Mechanism of Enhanced Conversion of 1,2,3-Trichloropropane by Mutant Haloalkane Dehalogenase Revealed by Molecular Modeling. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN. 2006, vol. 20, No 9, p. 375-383. ISSN 0920-654X.

KLVAŇA, Martin, R.C. WADE, Petr KULHÁNEK and Jiří DAMBORSKÝ. Modelling of Product Release and Identification of Export Routes in Haloalkane Dehalogenase DhaA. 2006.

FOŘTOVÁ, Andrea, Martina PAVLOVÁ, Martin KLVAŇA, Radka CHALOUPKOVÁ, Marta MONINCOVÁ, T. SATO, M. TSUDA, Yuji NAGATA and Jiří DAMBORSKÝ. Mycobacteria as a Source of Haloalkane Dehalogenases: Identification of the Catalytic Pentad within the Structure of DhmA from Mycobacterium avium N85. 2006.

DAMBORSKÝ, Jiří, Zbyněk PROKOP, Táňa KOUDELÁKOVÁ, Tomáš MOZGA, Petr JEŘÁBEK, Yukari SATO, Yuji NAGATA and T. SENDA. Natural and Engineered Enantioselective Haloalkane Dehalogenases. 2006.

HRADECKÝ, Jan, Radka MIKELOVÁ, Zbyněk PROKOP, Libuše TRNKOVÁ, Jiří DAMBORSKÝ, Vojtěch ADAM, Jitka PETRLOVÁ and René KIZEK. Navržení Biosenzoru pro detekci chlorovaných pesticidů (Development of Biosensor for determination of chlorinated pesticides). In Sborník příspěvků VI. Pracovního setkání fyzikálních chemiků a elektrochemiků. Brno: Masarykova universita, 2006, p. 50-51, 125 pp. ISBN 80-210-3943-4.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Monika STRAKOVÁ, Tomáš MOZGA and Jiří DAMBORSKÝ. Physical Variables as a Control of Enzyme Stereoselectivity. 2006.

MONINCOVÁ, Marta, Yuji NAGATA, Radka CHALOUPKOVÁ, Zbyněk PROKOP, Andrea FOŘTOVÁ, Martina PAVLOVÁ, Masataka TSUDA and Jiří DAMBORSKÝ. Protein engineering of haloalkane dehalogenase LinB: reconstruction of active site and modification of entrance tunnel. In Book of Abstracts, 10th International Symposium of the Genetics of Industrial Microorganisms. 1st ed. Praha: Institute of Microbiology ASCR, 2006, p. 160-161. ISBN 80-239-7323-1.

DAMBORSKÝ, Jiří. Proteinové inženýrství enzymů (Protein Engenneering of Enzymes). 2006.

GROCHOVÁ, Diana, Jana VAŇKOVÁ, Jiří DAMBORSKÝ and Jana ŠMARDOVÁ. Reaktivace proteinu p53 pomocí Amifostinu - experimentální studie v kvasinkovém expresním systému (Re-activation of the p53 protein by Amifostine - the experimental study in the yeast expression system). In ABSTRAKTA. Olomouc: Univerzita Palackého Olomouc, 2006, p. 21-22. ISBN 80-239-8240-0.

POSPÍŠILOVÁ, Šárka, Jitka MALČÍKOVÁ, Jiří DAMBORSKÝ, Jana ŠMARDOVÁ, Martin TRBUŠEK, Boris TICHÝ, Yvona BRYCHTOVÁ, Michael DOUBEK and Jiří VORLÍČEK. Role of p53 Gene Mutation Type in B-CLL Prognosis. 2006.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Monika STRAKOVÁ, Tomáš MOZGA and Jiří DAMBORSKÝ. Řízení stereoselektivity enzymu fyzikálně-chemickými parametry (Direction of Enzymes Stereoselectivity by physical-chemical Parameters.). 2006.

PAPAJAK, Ewa, Zbyněk PROKOP, Radka CHALOUPKOVÁ, Jiří DAMBORSKÝ and Piotr PANETH. Solvent Isotope Effects on Haloalkane Dehalogenase LinB. 2006.

MONINCOVÁ, Marta, Radka CHALOUPKOVÁ, Yuji NAGATA, Zbyněk PROKOP, Soňa MARVANOVÁ, Jana SÝKOROVÁ, Andrea JESENSKÁ, Martina PAVLOVÁ, M. TSUDA and Jiří DAMBORSKÝ. Structure-Based Engineering of Haloalkane Dehalogenase. 2006.

PAVLOVÁ, Martina, Martin KLVAŇA, Andrea JESENSKÁ, Zbyněk PROKOP, Hana KONEČNÁ, T. SATO, M. TSUDA, Yuji NAGATA and Jiří DAMBORSKÝ. The Identification of Catalytic Pentad in the Haloalkane Dehalogenase DhmA from Mycobacterium avium N85: Reaction Mechanism and Molecular Evolution. JOURNAL OF STRUCTURAL BIOLOGY. 2006, 1/2006, No 1, p. 9999-10007. ISSN 1047-8477.

DAMBORSKÝ, Jiří. The Past, the Present and the Future of Czech Biotechnologies. 2006.

CHALOUPKOVÁ, Radka, Zbyněk PROKOP, Monika STRAKOVÁ, Tomáš MOZGA and Jiří DAMBORSKÝ. The stereoselectivity and Conformational Stability of Haloalkane Dehalogenase DbjA from Bradyrhizobium japonicum USDA110: The Effect of Temperature and pH. 2006.

HRADECKÝ, Jan, Radka MIKELOVÁ, Zbyněk PROKOP, Libuše TRNKOVÁ, Jiří DAMBORSKÝ, Vojtěch ADAM and René KIZEK. Vyvoj enzymoveho biosenzoru pro detekci chlorovanych pesticidu (A suggestion of enzymatic biosensor for determination of chlorinated pesticides). In VI. Mezioborove setkani mladych biologu, biochemiku a chemiku; Sigma-Aldrich. první. Praha: Ceska spolecnost chemicka, 2006, p. 384-385. ISSN 0009-2770.

LOCHMAN, Jan, Tomáš KAŠPAROVSKÝ, Jiří DAMBORSKÝ, Hanan OSMAN, MIchel PONCHET, Vladimír MIKEŠ and Radka CHALOUPKOVÁ. Construction of Cryptogein Mutants, a Proteinaceous Elicitor from Phytophthora, with Altered Abilities To Induce a Defense Reaction in Tobacco Cells. Biochemistry. USA, 2005, vol. 44, No 17, p. 6565-6577. ISSN 0006-2960.

NAGATA, Yuji, Zbyněk PROKOP, Yukari SATO, Petr JEŘÁBEK, Ashawi KUMAR, Yoshiyuhi OHTSUBO, Masataka TSUDA and Jiří DAMBORSKÝ. Degradation of b-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26. Applied and Environmental Microbiology. USA, 2005, vol. 71, No 4, p. 2183-2185. ISSN 0099-2240.

JESENSKÁ, Andrea, Martina PAVLOVÁ, Michal STROUHAL, Radka CHALOUPKOVÁ, Iva TĚŠÍNSKÁ, Marta MONINCOVÁ, Zbyněk PROKOP, Milan BARTOŠ, Ivo PAVLÍK, Ivan RYCHLÍK, Petra MOBIUS, Yuji NAGATA and Jiří DAMBORSKÝ. Mycobacterial Haloalkane Dehalogenases: Cloning, Biochemical Properties and distribution. Applied and Environmental Microbiology. 2005, vol. 71, No 11, p. 6736-6745. ISSN 0099-2240.

KMUNÍČEK, Jan, Kamila HYNKOVÁ, Tomáš JEDLIČKA, Yuji NAGATA, Ana NEGRI, Frederico GAGO, Rebecca WADE and Jiří DAMBORSKÝ. Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26. Biochemistry. 2005, vol. 9, No 44, p. 3390-3401. ISSN 0006-2960.

PROKOP, Martin, Jiří DAMBORSKÝ and Jaroslav KOČA. TRITON: graphic software for modelling protein mutants and calculation reaction pathways. In Materials Structure in Chemistry, Biology, Physics and Technology. vol.12, no. 1. Praha: Czech and Slovak Crystallographic Association, 2005, p. 17. ISSN 1211-5894.

SATO, Yukari, Marta MONINCOVÁ, Radka CHALOUPKOVÁ, Zbyněk PROKOP, Yoshiyuki OHTSUBO, Kiwamu MINAMISAWA, Masataka TSUDA, Jiří DAMBORSKÝ and Yuji NAGATA. Two Rhizobial Strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, Encode Haloalkane Dehalogenases with Novel Structures and Substrate Specificities. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 2005, vol. 71, No 8, p. 43724379-43724386. ISSN 0099-2240.

HRADECKÝ, Jan, Radka MIKELOVÁ, Zbyněk PROKOP, Libuše TRNKOVÁ, Jiří DAMBORSKÝ, Vojtěch ADAM, Jitka PETRLOVÁ and René KIZEK. Vývoj enzymového biosenzoru pro detekci chlorovaných pesticidů (Development of enzym biosenzor for detection of chlorinated pesticides). In Sborník příspěvků: MendelNet 2005. Brno: Mendelova zemedelska a lesnicka univerzita v Brně, 2005, p. 61-61, 139 pp. ISBN 80-7157-905-X.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, František OPLUŠTIL, Andrea JESENSKÁ and Yuji NAGATA. Způsob detoxikace sulfidického yperitu psobením halogenalkandehalogenázami (Method of detoxification of yperite by using haloalkane dehalogenases). 2005.

PROKOP, Zbyněk, Jiří DAMBORSKÝ, Dick JANSSEN and Yuji NAGATA. Způsob výroby opticky aktivních halogenalkanů a alkoholů hydrolytickou dehalogenací katalyzovanou halogenalkandehalogenázami (METHOD OF PRODUCTION OF OPTICALLY ACTIVE HALOHYDROCARBONS AND ALCOHOLS USING HYDROLYTIC DEHALOGENATION CATALYSED BY HALOALKANE DEHALOGENASES). 2005.

DAMBORSKÝ, Jiří. Alfred Bader - Chemist and Art Collector. 2004.

DOBES, Petr, Jan KMUNÍČEK, Vladimír MIKEŠ and Jiří DAMBORSKÝ. Binding of Fatty Acids to b-Cryptogein: Quantitative Structure-Activity Relationships and Design of Selective Protein Mutants. Journal of Chemical Information and Modeling. USA, 2004, 44-6, No 44, p. 2126-2132. ISSN 1549-960X.

DAMBORSKÝ, Jiří. Bioinformatics II. 2004.

OAKLEY, Aaron, Martin KLVAŇA, Michal OTYEPKA, Yuji NAGATA, Matthew WILCE and Jiří DAMBORSKÝ. Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A Resolution: Dynamics of Catalytic Residues. Biochemistry. USA, 2004, vol. 43, No 43, p. 870-878, 8 pp. ISSN 0006-2960.

ŠTEKROVÁ, Jitka, Jana REITEROVÁ, Miroslav MERTA, Jiří DAMBORSKÝ, Jana ŽÍDOVSKÁ, Věra KEBRDLOVÁ and Milada KOHOUTOVÁ. PKD2 Mutations in Czech Population with Autosomal Dominant Polycystic Kidney Disease. Nephrology Dialysis Transplantation. UK, 2004, vol. 2004, No 19, p. 1116-1122. ISSN 1460-2385.

ERIKSSON, Lennart, Jiří DAMBORSKÝ, Matthew EARLL, Erik JOHANSSON, Johan TRYGG and Svante WOLD. Three-Block Bi-Focal PLS (3BIF-PLS) and its Application in QSAR. SAR and QSAR in Environmental Research. USA, 2004, 5-6, No 15, p. 481-499, 18 pp. ISSN 1062-936X.

PROKOP, Zbyněk, Marta MONINCOVÁ, Radka CHALOUPKOVÁ, Martin KLVAŇA, Yuji NAGATA, Dick B. JANSSEN and Jiří DAMBORSKÝ. Catalytic mechanism of the haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. Journal of Biological Chemistry. 2003, vol. 278, No 46, p. 45094-45100. ISSN 0021-9258.

HATTA, Takashi, Gouri MUKERJEE-DHAR, Jiri DAMBORSKY, Hohzoh KIYOHARA and Kazuhide KIMBARA. Cloning and characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a PCB and naphthalene degrading Bacillus sp. JF8. Journal of Biological Chemistry. 2003, vol. 278, No 24, p. 21483-21492. ISSN 0021-9258.

KMUNÍČEK, Jan, Michal BOHÁČ, Santos LUENGO, Federico GAGO, Rebecca WADE and Jiří DAMBORSKÝ. Comparative binding energy analysis of haloalkane dehalogenase substrates: modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. Journal of Computer-Aided Molecular Design. 2003, vol. 17, No 5, p. 299-311. ISSN 0920-654X.

STRELTSOV, Victor, Zbyněk PROKOP, Jiří DAMBORSKÝ, Yuji NAGATA, Aaron OAKLEY and Matthew C.J. WILCE. Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates. Biochemistry. 2003, vol. 42, No 34, p. 10104-10112. ISSN 0006-2960.

CHALOUPKOVÁ, Radka, Jana SÝKOROVÁ, Zbyněk PROKOP, Andrea JESENSKÁ, Marta MONINCOVÁ, Martina PAVLOVÁ, Masataka TSUDA, Yuji NAGATA and Jiří DAMBORSKÝ. Modification of Activity and Specificity of Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26 by Engineering of its Entrance Tunnel. Journal of Biological Chemistry. 2003, vol. 278, No 52, p. 52622-52628. ISSN 1083-351X.

DAMBORSKÝ, Jiří, Jan KMUNÍČEK, Tomáš JEDLIČKA, Santos LUENGO, Federico GAGO, Angel R. ORTIZ and Rebecca C. WADE. Rational re-design of haloalkane dehalogenases guided by comparative binding energy analysis. In Enzyme Functionality: Design, Engineering and Screening. New York, USA: Marcel Decker, 2003, p. 79-96. Protein Structure.

NAGATA, Yuji, Zbyněk PROKOP, Soňa MARVANOVÁ, Jana SÝKOROVÁ, Marta MONINCOVÁ, Masataka TSUDA and Jiří DAMBORSKÝ. Re-construction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB. Applied and Environmental Microbiology. 2003, vol. 69, No 4, p. 2349-2355. ISSN 1098-5336.

MATIASOVIČOVÁ, Jitka, Marcela FALDYNOVÁ, Martina PRAVCOVÁ, Renata KARPÍŠKOVÁ, Ivana KOLÁČKOVÁ, Jiří DAMBORSKÝ and Ivan RYCHLÍK. Retron reverse transcriptase rrtT is ubiquitous in strains of Salmonella enterica serovar Typhimurium. FEMS Microbiology Letters. 2003, vol. 223, No 2, p. 281-286. ISSN 0378-1097.

MONINCOVÁ, Marta, Yuji NAGATA, Zbyněk PROKOP, Soňa MARVANOVÁ, Jana SÝKOROVÁ, Masataka TSUDA and Jiří DAMBORSKÝ. Validation of Putative Enzymes from Genomic Projects: Confirmation of Dehalogenation ARv2ctivity for Mycobacterial Protein 579 (Validation of Putative Enzymes from Genomic Projects: Confirmation of Dehalogenation Activity for Mycobacterial Protein Rv2579). In Management and Control of (Undesirable) Microorganisms, IBBS/IBRG Meeting Abstracts. Manchester, UK: IBBS/IBRG, 2003, p. 28.

BOSMA, Tjibbe, Jiří DAMBORSKÝ, Gerhard STUCKI and Dick JANSSEN. Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene. Applied and Environmental Microbiology. 2002, vol. 68, No 7, p. 3582-3587. ISSN 1098-5336.

JESENSKÁ, Andrea, Milan BARTOŠ, Vladimíra CZERNEKOVÁ, Ivan RYCHLÍK, Ivo PAVLÍK and Jiří DAMBORSKÝ. Cloning, expression and preliminary characterization of novel haloalkane dehalogenase DhmA from Mycobacterium avium N85. Applied and Environmental Microbiology. 2002, vol. 68, No 8, p. 3724-7453. ISSN 1098-5336.

OAKLEY, Aaron, Zbyněk PROKOP, Michal BOHÁČ, Jan KMUNÍČEK, Tomáš JEDLIČKA, Marta MONINCOVÁ, Ivana KUTÁ-SMATANOVÁ, Yuji NAGATA, Jiří DAMBORSKÝ and Matthew WILCE. Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product and water mediated inhibition. Biochemistry. 2002, vol. 41, No 15, p. 4847-4855. ISSN 0006-2960.

OTYEPKA, Michal and Jiří DAMBORSKÝ. Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains. Protein Science. 2002, vol. 11, No 5, p. 1206-1217. ISSN 0961-8368.

BOHÁČ, Michal, Yuji NAGATA, Zbyněk PROKOP, Martin PROKOP, Marta MONINCOVÁ, Masataka TSUDA, Jaroslav KOČA and Jiri DAMBORSKÝ. Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis. Biochemistry. 2002, vol. 41, No 48, p. 14272-14280. ISSN 0006-2960.

RYCHLÍK, Ivan, Martin GERALD, Ulrich METHNER, Margaret LOVELL, Lenka CRDOVÁ, Alena SBKOVÁ, Mojmír SEVCIK, Jiri DAMBORSKÝ and Paul BARROW. Identification of Salmonella enterica serovar Typhimurium genes associated with growth suppression in stationary-phase nutrient broth cultures and in the chicken intestine. Archives of Microbiology. 2002, vol. 178, No 6, p. 411-420. ISSN 0302-8933.

BOHÁČ, Michal, Bjorn LOEPRECHT, Jiří DAMBORSKÝ and Gerrit SCHUURMANN. Impact of Orthogonal Signal Correction (OSC) on the predictive ability of CoMFA models for the ciliate toxicity of nitrobenzenes. Quantitative Structure-Activity Relationships. 2002, vol. 21, No 1, p. 3-11. ISSN 0931-8771.

VOLF, Jiří, Mojmír ŠEVČÍK, Hana HAVLÍČKOVÁ, František ŠIŠÁK, Jiří DAMBORSKÝ and Ivan RYCHLÍK. Role of SdiA in Salmonella enterica serovar typhimurium physiology and virulence. Archives in Microbiology. 2002, vol. 178, No 2, p. 94-101. ISSN 0302-8933.

MARVANOVÁ, Soňa, Yuji NAGATA, Michaela WIMMEROVÁ, Jana SÝKOROVÁ, Kamila HYNKOVÁ and Jiří DAMBORSKÝ. Biochemical characterization of broad-specificity enzymes using multivariate experimental design and a colorimetric microplate assay: characterization of the haloalkane dehalogenase mutants. Journal of Microbiological Methods. 2001, vol. 44, No 1, p. 149-157. ISSN 0167-7012.

KMUNÍČEK, Jan, Santos LUENGO, Federico GAGO, Angel Ramirez ORTIZ, Rebecca WADE and Jiří DAMBORSKÝ. Comparative binding energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. Biochemistry. 2001, vol. 40, No 30, p. 8905-8917. ISSN 0006-2960.

MACHÁČKOVÁ, Eva, Jiří DAMBORSKÝ, Dalibor VALÍK and Lenka FORETOVÁ. Four novel germline BRCA1 and BRCA2 mutations in breast and breast-ovarian cancer. Human Mutation. 2001, vol. 18, No 1, p. 545-549. ISSN 1059-7794.

NAGATA, Yuji, Katsuki MORI, Masamichi TAKAGI, Alexey G. MURZIN and Jiri DAMBORSKY. Identification of protein fold and catalytic residues of g-hexachlorocyclohexane dehydrochlorinase LinA. PROTEINS: Structure, Function, and Genetics. 2001, vol. 45, No 4, p. 471-477.

ZOUHAR, Jan, Jitka VÉVODOVÁ, Jaromír MAREK, Jiří DAMBORSKÝ, X.-D. SU and Břetislav BRZOBOHATÝ. Insights into the Functional Architecture of the Catalytic Center of a Maize Beta-Glucosidase Zm-p60.1. Plant Physiology. USA: American Society of Plant Physiologists, 2001, vol. 127, No 3, p. 973-985. ISSN 0032-0889.

KREJČÍ, Lumír, Jiří DAMBORSKÝ, B. THOMSEN, M. DUNO and C. BENDIXEN. Molecular dissection of interactions between Rad51 and members of the recombination-repair group (olecular dissection of interactions between Rad51 and members of the recombination-repair group). Molecular and Cellular Biology. 2001, vol. 21, No 3, p. 966-976. ISSN 0270-7306.

JANDA, Lubomír, Jiří DAMBORSKÝ, Gerhard A. REZNICZEK and Gerhard WICHE. Plectin repeats and modules: strategic cysteines and their presumed impact on cytolinker. Bioessays. 2001, vol. 23, No 11, p. 1064-1069.

TRANTÍREK, Lukáš, Kamila HYNKOVÁ, Yuji NAGATA, Alexey MURZIN, Alena ANSORGOVÁ, Vladimír SKLENÁŘ and Jiří DAMBORSKÝ. Reaction mechanism and stereochemistry of gamma-hexachlorocyclohexane dehydrochlorinase LinA. Journal of Biological Chemistry. 2001, vol. 276, No 11, p. 7734-7740.

DAMBORSKÝ, Jiří, Emiel RORIJE, Andrea JESENSKÁ, Yuji NAGATA, Gilles KLOPMAN and Willie PEIJNENBURG. Structure-specificity relationships for haloalkane dehalogenases. Environmental Toxicology and Chemistry. 2001, vol. 20, No 12, p. 2681-2689.

DAMBORSKÝ, Jiří, Martin PROKOP and Jaroslav KOČA. TRITON: graphic software for rational engineering of enzymes. Trends in Biochemical Sciences. 2001, vol. 28, No 1, p. 71-73.

MAREK, Jaromír, Jitka VÉVODOVÁ, Ivana KUTÁ-SMATANOVÁ, Y. NAGATA, L.A. SVENSSON, J. NEWMAN, M. TAKAGI and Jiří DAMBORSKÝ. Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry. Washington, DC, USA: American Chemical Society, 2000, vol. 39, No 46, p. 14082-14086. ISSN 0006-2960.