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.

NEKULOVÁ, Marta, Marta WYSZKOWSKA, Nela FRIEDLOVÁ, Lukáš UHRÍK, Filip ZAVADIL KOKÁŠ, Václav HRABAL, Lenka HERNYCHOVÁ, Bořivoj VOJTĚŠEK, Ted R. HUPP and Michał SZYMAŃSKI. Biochemical evidence for conformational variants in the anti-viral and pro-metastatic protein IFITM1. BIOLOGICAL CHEMISTRY. GERMANY: WALTER DE GRUYTER GMBH, 2024. ISSN 1431-6730. Available from: https://dx.doi.org/10.1515/hsz-2023-0327.

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.

NYKODÝMOVÁ, Daniela, Lenka MOLČANOVÁ, Jan KOTOUČEK, Josef MAŠEK and Jakub TREML. Determination of PPAR gamma agonistic activity of mimulone and diplacone in nanoparticle formulations. In PSE Trends in Natural Products 2024 Young Scientists' Meeting. 2024. ISBN 978-80-280-0559-7.

EGHBALINEJAD, Mahleh, María del Rocío LÓPEZ CABEZA, Jan KOTOUČEK, Renato GRILLO, Marek KOUTNY, Zuzana HOCHMANOVÁ and Jakub HOFMAN. Effects of three tebuconazole nanopesticides on the survival of <i>Daphnia magna</i>. Environmental Science: Nano. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2024, vol. 11, No 3, p. 1044-1059. ISSN 2051-8153. Available from: https://dx.doi.org/10.1039/d3en00673e.

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.

HARDING-LARSEN, David, Christian Degnbol MADSEN, David TEZE, Tiia KITTILA, Mads Rosander LANGHORN, Hani GHARABLI, Mandy HOBUSCH, Felipe Mejia OTALVARO, Onur KIRTEL, Gonzalo Nahuel BIDART, Stanislav MAZURENKO, Evelyn TRAVNIK and Ditte Hededam WELNER. GASP: A Pan-Specific Predictor of Family 1 Glycosyltransferase Acceptor Specificity Enabled by a Pipeline for Substrate Feature Generation and Large-Scale Experimental Screening. ACS Omega. WASHINGTON: American Chemical Society, 2024, vol. 9, No 25, p. 27278-27288. ISSN 2470-1343. Available from: https://dx.doi.org/10.1021/acsomega.4c01583.

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.

MIKUŠOVÁ, Petra, Zuzana TOUŠOVÁ, Luděk SEHNAL, Jan KUTA, K. GRABICOVA, G. FEDOROVA, Martin MAREK, R. GRABIC and Klára HILSCHEROVÁ. Identification of new endocrine disruptive transthyretin ligands in polluted waters using pull-down assay coupled to non-target mass spectrometry. Journal of Hazardous Materials. Amsterdam: Elsevier Science BV., 2024, vol. 471, June 2024, p. 1-12. ISSN 0304-3894. Available from: https://dx.doi.org/10.1016/j.jhazmat.2024.134240.

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.

BOUDNÁ, Marie, Táňa MACHÁČKOVÁ, Petra VYCHYTILOVÁ, Karolína TRACHTOVÁ, Renata BARTOŠOVÁ, Tina CATELA IVKOVIĆ, Dagmar AL TUKMACHI, Robin JUGAS, Lucie PIFKOVÁ, Jana ORLÍČKOVÁ, Jan KOTOUČEK, Marketa PAVLIKOVA, Milana ŠACHLOVÁ, Lucia BOHOVICOVÁ, Teodor STANĚK, Jana HALÁMKOVÁ, Igor KISS, Tomáš GROLICH, Martin SVOBODA, Zdeněk KALA, Kamila SOUČKOVÁ and Ondřej SLABÝ. Investigation of long non-coding RNAs in extracellular vesicles from low-volume blood serum specimens of colorectal cancer patients. CLINICAL AND EXPERIMENTAL MEDICINE. MILAN: SPRINGER-VERLAG ITALIA SRL, 2024, vol. 24, No 1, p. 1-14. ISSN 1591-8890. Available from: https://dx.doi.org/10.1007/s10238-024-01323-1.

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.

SMOLKO, Martin, Ondrej KOVÁČ, Anna VYHLÍDALOVÁ KOTRBOVÁ, Nina BÖHMEOVÁ, Anežka CELÁ, Jan KOTOUČEK, Karel SOUČEK, Vítězslav BRYJA and Vendula HLAVÁČKOVÁ POSPÍCHALOVÁ. Lipidomic analysis of tetraspanin-deficient extracellular vesicles. In XXVII. BIOLOGICKÉ DNY - TKÁŇOVÉ MIKROPROSTŘEDÍ. 2024.

SMOLKO, Martin, Ondrej KOVÁČ, Anna VYHLÍDALOVÁ KOTRBOVÁ, Nina BÖHMEOVÁ, Anežka CELÁ, Jan KOTOUČEK, Karel SOUČEK, Vítězslav BRYJA and Vendula HLAVÁČKOVÁ POSPÍCHALOVÁ. Lipidomic profiling of extracellular vesicles from tetraspanin-deficient cell lines. In ASEV-CzeSEV Joint Meeting on Extracellular Vesicles. 2024.

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.

EGHBALINEJAD, Mahleh, Jakub HOFMAN, Jan KOTOUČEK, Renato GRILLO, Zuzana HOCHMANOVÁ, Nicola REIFF and Sebastian HOESS. Nano-enabled pesticides: a comprehensive toxicity assessment of tebuconazole nanoformulations with nematodes at single species and community level. Jakub Hofman, Jan Kotouček, Renato Grillo, Zuzana Hochmanová Bílková, Nicola Re. Environmental Sciences Europe. NEW YORK: Springer-Verlag, GmbH, Environmental Sciences Europe, 2024, vol. 36, No 1, p. 1-16. ISSN 2190-4707. Available from: https://dx.doi.org/10.1186/s12302-024-00879-9.

BENEŠOVÁ, Iva, Rudolf NENUTIL, Adam Paulin URMINSKÝ, Erika LATTOVÁ, Lukas UHRIK, Peter GRELL, Filip Zavadil KOKAS, Jana HALÁMKOVÁ, Zbyněk ZDRÁHAL, Bořivoj VOJTĚŠEK, Miloš V NOVOTNÝ and Lenka HERNYCHOVÁ. N-glycan profiling of tissue samples to aid breast cancer subtyping. Nature Scientific Reports. London: NATURE RESEARCH, 2024. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-023-51021-3.

VYCHYTILOVÁ, Petra, Sára VILMANOVÁ, Lucie PIFKOVÁ, Tina CATELA IVKOVIĆ, Marie MĄDRZYK, Robin JUGAS, Táňa MACHÁČKOVÁ, Jan KOTOUČEK, Milana ŠACHLOVÁ, Lucia BOHOVICOVÁ, Teodor STANĚK, Jana HALÁMKOVÁ, Igor KISS and Ondřej SLABÝ. Optimized procedure for high-throughput transcriptome profiling of small extracellular vesicles isolated from low volume serum samples. Clinical Chemistry and Laboratory Medicine. Berlin: WALTER DE GRUYTER, 2024, vol. 62, No 1, p. 157-167. ISSN 1434-6621. Available from: https://dx.doi.org/10.1515/cclm-2023-0610.

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.

RAKYTOVÁ, Janka, Martin SMOLKO, Anna VYHLÍDALOVÁ KOTRBOVÁ, Kristína GÖMÖRYOVÁ, Anežka CELÁ, Jan KOTOUČEK, Václav PUSTKA, Zbyněk ZDRÁHAL, Karel SOUČEK, Vítězslav BRYJA and Vendula HLAVÁČKOVÁ POSPÍCHALOVÁ. Proteomic analysis of tetraspanin-deficient extracellular vesicles. In ASEV-CzeSEV Joint Meeting on Extracellular Vesicles. 2024.

LÓPEZ CABEZA, María del Rocío, Mahleh EGHBALINEJAD, Melanie KAH, Renato GRILLO, Zuzana HOCHMANOVÁ, Jan KOTOUČEK and Jakub HOFMAN. Release and stability of two tebuconazole nanoformulations in different aquatic media. Environmental Science: Nano. CAMBRIDGE: ROYAL SOC CHEMISTRY, 2024, vol. 11, No 4, p. 1612-1621. ISSN 2051-8153. Available from: https://dx.doi.org/10.1039/d3en00790a.

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.

MARTIN, Hector Garcia, Stanislav MAZURENKO and Huimin ZHAO. Special Issue on Artificial Intelligence for Synthetic Biology. ACS Synthetic Biology. American Chemical Society, 2024, vol. 13, No 2, p. 408-410. ISSN 2161-5063. Available from: https://dx.doi.org/10.1021/acssynbio.3c00760.

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.

POLJOVKA, Andrej, Miloš MUSIL, David BEDNÁŘ, Katarina CHOVANOVA, Vladena BAUEROVA-HLINKOVA, Jana BELLOVA, Lenka KOHUTOVA, Peter BARATH and Marcel ZAMOCKY. Comparison of Fungal Thermophilic and Mesophilic Catalase-Peroxidases for Their Antioxidative Properties. Antioxidants. Basel: MDPI, 2023, vol. 12, No 7, p. 1-19. ISSN 2076-3921. Available from: https://dx.doi.org/10.3390/antiox12071382.

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.

SMOLKO, Martin, Anna VYHLÍDALOVÁ KOTRBOVÁ, Anežka CELÁ, Jan KOTOUČEK, Karel SOUČEK, Vítězslav BRYJA and Vendula HLAVÁČKOVÁ POSPÍCHALOVÁ. CRISPR CAS9 ENGINEERED TETRASPANIN DEFICIENT CELL LINES FOR THE ANALYSIS OF EXTRACELLULAR VESICLES. In 12th International Conference Analytical Cytometry. 2023.

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.

GUERRA-SLOMPO, Eloise Pavao, Gisele Fernanda Assine PICCHI-CONSTANTE, Martin MAREK, Christophe ROMIER, Wolfgang SIPPL and Nilson Ivo Tonin ZANCHIN. In cellulo and in vivo assays for compound testing against Trypanosoma cruzi. STAR Protocols. United States: Cell Press, 2023, vol. 4, No 1, p. 1-42. ISSN 2666-1667. Available from: https://dx.doi.org/10.1016/j.xpro.2023.102058.

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.

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.

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.

ONUŠČÁKOVÁ, Magdaléna, Hana PÍŽOVÁ, Tereza KAUEROVÁ, Marie HAMŠÍKOVÁ, David BEDNÁŘ, Peter KOLLÁR and Pavel BOBÁĽ. DESIGN AND SYNTHESIS OF N-HYDROXY-CINNAMAMIDE DERIVATES AS NOVEL HDAC INHIBITORS: EVALUATION OF BIOLOGICAL ACTIVITY IN CANCER CELLS. Online. In Radmila Řápková, Martin Fusek, Pavel Drašar. Czech Chemical Society Symposium Series. Pague, Czech republic: Czech Chemical Society, 2022, p. 28-29. ISSN 2336-7202.

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.

HOŘÁK, Martin, DeLisa FAIRWEATHER, Piia Pauliina KOKKONEN, David BEDNÁŘ and Julie DOBROVOLNÁ. Follistatin-like 1 and its paralogs in heart development and cardiovascular disease. Heart Failure Reviews. New York: Springer US, 2022, vol. 27, No 6, p. 2251-2265. ISSN 1382-4147. Available from: https://dx.doi.org/10.1007/s10741-022-10262-6.

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.

BENEŠOVÁ, Iva, Adam Paulin URMINSKÝ, Jana HALÁMKOVÁ and Lenka HERNYCHOVÁ. Changes of serum protein N-glycosylation in cancer. Časopis Klinická onkologie. Praha: Česká lékařská společnost J. E. Purkyně, 2022, vol. 35, No 3, p. 174-180. ISSN 0862-495X. Available from: https://dx.doi.org/10.48095/ccko2022174.

FRIEDLOVÁ, Nela, Lenka DOSEDĚLOVÁ, Filip ZAVADIL KOKÁŠ, Lenka HERNYCHOVÁ, Ted HUPP, Bořivoj VOJTĚŠEK and Marta NEKULOVÁ. IFITM PROTEINS REGULATE IMMUNE-RELATED CELL SURFACE MOLECULES IN CERVICAL CARCINOMA. 2022.

FRIEDLOVÁ, Nela, Michaela GALIOVÁ VAŠINOVÁ, Kristýna BILAVČÍKOVÁ, Pavel COUFALÍK, Lenka HERNYCHOVÁ, Vlastimil TICHÝ, Ted HUPP, Bořivoj VOJTĚŠEK and Marta NEKULOVÁ. IFITM PROTEINS REGULATE SENSITIVITY OF CERVICAL CANCER CELLS TO CISPLATIN. In XXI. Interdisciplinary meeting of young life scientists. 2022. ISSN 2336-7202.

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.

NĚMCOVÁ, Petra, Jana HOZZOVÁ and Jiří FILIPOVIČ. Improving ligand transport trajectory within flexible receptor in CaverDock. Online. In SAC '22: Proceedings of the 37th ACM/SIGAPP Symposium on Applied Computing. USA: Association for Computing Machinery, 2022, p. 619-626. ISBN 978-1-4503-8713-2. Available from: https://dx.doi.org/10.1145/3477314.3506988.

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.

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.

TRAPL, Dalibor, MArtin KRUPIČKA, Vladimír VIŠŇOVSKÝ, Jana HOZZOVÁ, Jaroslav OĽHA, Aleš KŘENEK and Vojtěch SPIWOK. Property Map Collective Variable as a Useful Tool for a Force Field Correction. Journal of Chemical Information and Modeling. American Chemical Society, 2022, vol. 62, No 3, p. 567-576. ISSN 1549-9596. Available from: https://dx.doi.org/10.1021/acs.jcim.1c00651.

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.

FILIPOVIČ, Jiří, Jana HOZZOVÁ, Amin NEZARAT, Jaroslav OĽHA and Filip PETROVIČ. Using hardware performance counters to speed up autotuning convergence on GPUs. Journal of Parallel and Distributed Computing. Elsevier, 2022, vol. 160, February, p. 16-35. ISSN 0743-7315. Available from: https://dx.doi.org/10.1016/j.jpdc.2021.10.003.

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.

VIŠŇOVSKÝ, Vladimír, Viktória SPIŠAKOVÁ, Jana HOZZOVÁ, Jaroslav OĽHA, Dalibor TRAPL, Vojtěch SPIWOK, Lukáš HEJTMÁNEK and Aleš KŘENEK. Complex simulation workflows in containerized high-performance environment. In Armenia S., Geril P. Proc. ESM 2021. Brusel: EUROSIS, 2021, p. 42-45. ISBN 978-94-92859-18-1.

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.

SABANDO, María Virginia, Pavol ULBRICH, Matías SELZER, Jan BYŠKA, Jan MIČAN, Ignacio PONZONI, Axel J. SOTO, María Luján GANUZA and Barbora KOZLÍKOVÁ. ChemVA: Interactive Visual Analysis of Chemical Compound Similarity in Virtual Screening. IEEE Transactions on Visualization and Computer Graphics. IEEE, 2021, vol. 27, No 2, p. 891-901. ISSN 1077-2626. Available from: https://dx.doi.org/10.1109/TVCG.2020.3030438.

PETROVIČ, Filip, Jiří FILIPOVIČ, David STŘELÁK, Jana HOZZOVÁ and Richard TREMBECKÝ. Kernel Tuning Toolkit 2.0. 2021.

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.

CLASON, Christian, Stanislav MAZURENKO and Tuomo VALKONEN. Primal-Dual Proximal Splitting and Generalized Conjugation in Non-smooth Non-convex Optimization. Applied Mathematics and Optimization. New York: Springer, 2021, vol. 84, No 2, p. 1239-1284. ISSN 0095-4616. Available from: https://dx.doi.org/10.1007/s00245-020-09676-1.

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, Jiří FILIPOVIČ, Amin NEZARAT, Jaroslav OĽHA and Filip PETROVIČ. Searching CUDA code autotuning spaces with hardware performance counters: data from benchmarks running on various GPU architectures. Data in Brief. Elsevier, 2021, vol. 39, December, p. 1-12. ISSN 2352-3409. Available from: https://dx.doi.org/10.1016/j.dib.2021.107631.

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.

MAREK, Martin, E. RAMOS-MORALES, G.F.A. PICCHI-CONSTANTE, T. BAYER, C. NORSTROM, D. HERP, P.A. SALES, E.P. GUERRA-SLOMPO, K. HAUSMANN, A. CHAKRABARTI, T.B. SHAIK, A. MERZ, E. TROESCH, K. SCHMIDTKUNZ, S. GOLDENBERG, R.J. PIERCE, MM MOURAO, M.M. JUNG, J. SCHULTZ, W. SIPPL, N.I.T. ZANCHIN and C. ROMIER. Species-selective targeting of pathogens revealed by the atypical structure and active site of Trypanosoma cruzi histone deacetylase DAC2. Cell Reports. CAMBRIDGE: Cell Press, 2021, vol. 37, No 12, p. 1-17, "e1-e9", 26 pp. ISSN 2211-1247. Available from: https://dx.doi.org/10.1016/j.celrep.2021.110129.

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.

RAMOS-MORALES, Elizabeth, Efil BAYAM, Jordi DEL-POZO-RODRIGUEZ, Thalia SALINAS-GIEGE, Martin MAREK, Ramos-Morales, E (Ramos- TILLY, Philippe WOLFF, Edouard TROESCH, Eric ENNIFAR, Laurence DROUARD, Juliette D. GODIN and Christophe ROMIER. The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Nucleic acids research. Oxford: Oxford University Press, 2021, vol. 49, No 11, p. 6529-6548. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkab436.

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.

FRIEDLOVÁ, Nela, Lenka DOSEDĚLOVÁ, Filip ZAVADIL KOKÁŠ, Lenka HERNYCHOVÁ, Bořivoj VOJTĚŠEK and Marta NEKULOVÁ. Vliv IFITM1 na „surfaceom“ buněk cervikálního karcinomu. In Brněnské onkologické dny. 2021. ISSN 0862-495X.

BRŮŽA, Vojtěch, Jan BYŠKA, Jan MIČAN and Barbora KOZLÍKOVÁ. VRdeo: Creating engaging educational material for asynchronous student-teacher exchange using virtual reality. COMPUTERS & GRAPHICS-UK. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD, 2021, vol. 98, August 2021, p. 280-292. ISSN 0097-8493. Available from: https://dx.doi.org/10.1016/j.cag.2021.06.009.

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.

BRÁZDIL, Tomáš, David PORTEŠ, Jiří FILIPOVIČ, Jana HOZZOVÁ, Thomas EVANGELIDIS and Konstantinos TRIPSIANES. 4D-GRAPHS. 2021.

PETROVIČ, Filip, David STŘELÁK, Jana HOZZOVÁ, Jaroslav OĽHA, Richard TREMBECKÝ, Siegfried BENKNER and Jiří FILIPOVIČ. A benchmark set of highly-efficient CUDA and OpenCL kernels and its dynamic autotuning with Kernel Tuning Toolkit. Future Generation Computer Systems. Elsevier, 2020, vol. 108, July, p. 161-177. ISSN 0167-739X. Available from: https://dx.doi.org/10.1016/j.future.2020.02.069.

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.

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.

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.

BEZDÍČEK, Matěj, Markéta NYKRÝNOVÁ, Kristýna DUFKOVÁ, Kristina PLEVOVÁ, Iva KOCMANOVÁ and Martina LENGEROVÁ. Epidemiology typing and molecular analysis of vancomycin-resistant Enterococcus foeclum in haemato-oncological patients. In 30th ECCMID 2020. 2020.

OĽHA, Jaroslav, Jana HOZZOVÁ, Jan FOUSEK and Jiří FILIPOVIČ. Exploiting historical data: Pruning autotuning spaces and estimating the number of tuning steps. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE. HOBOKEN: WILEY, 2020, vol. 32, No 21, p. 1-15. ISSN 1532-0626. Available from: https://dx.doi.org/10.1002/cpe.5962.

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.

KŘENEK, Aleš, Jana HOZZOVÁ, Jaroslav OĽHA, Dalibor TRAPL and Vojtěch SPIWOK. Exploring Protein Folding Space with Neural Network Guided Simulations. In Alexandre Nketsa. MODELLING AND SIMULATION 2020. Brusel: EUROSIS-ETI, 2020, p. 305-309. ISBN 978-94-92859-12-9.

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.

MAZURENKO, Stanislav. Predicting protein stability and solubility changes upon mutations: data perspective. ChemCatChem. Weinheim: Wiley-VCH GmbH, 2020, vol. 12, No 22, p. 5590-5598. ISSN 1867-3880. Available from: https://dx.doi.org/10.1002/cctc.202000933.

MAZURENKO, Stanislav, Jyrki JAUHIAINEN and Tuomo VALKONEN. Primal-dual block-proximal splitting for a class of non-convex problems. Electronic Transactions on Numerical Analysis. Kent: Kent State University, 2020, vol. 52, No 2020, p. 509-552. ISSN 1068-9613. Available from: https://dx.doi.org/10.1553/etna_vol52s509.

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.

LAHAM-KARAM, Nihay, José Gaspar RANGEL PAMPLONA PIZARRO PINTO, Antti POSO and Piia Pauliina KOKKONEN. Transcription and Translation Inhibitors in Cancer Treatment. Frontiers in Chemistry. Lausanne: Frontiers Media SA, 2020, vol. 8, April 2020, p. 1-24. ISSN 2296-2646. Available from: https://dx.doi.org/10.3389/fchem.2020.00276.

NÁLEŽINSKÁ, Monika, DUBSKÁ L ZDRAŽILOVÁ, Dalibor VALÍK, Lenka HERNYCHOVÁ, T PAVLÍK, M MAZALOVÁ, Josef CHOVANEC and Vuk FAIT. Úskalí laboratorních metod v ovariálním skríninku - doba "-omická"? Czech Yearbook of Public & Private International Law (Vol.11) - 2020 Read more: https://www.cyil.eu/contents-cyil-2020/. Praha: Czech Society of International Law, 2020.

CLASON, Christian, Stanislav MAZURENKO and Tuomo VALKONEN. ACCELERATION AND GLOBAL CONVERGENCE OF A FIRST-ORDER PRIMAL-DUAL METHOD FOR NONCONVEX PROBLEMS. SIAM JOURNAL ON OPTIMIZATION. PHILADELPHIA: SIAM PUBLICATIONS, 2019, vol. 29, No 1, p. 933-963. ISSN 1052-6234. Available from: https://dx.doi.org/10.1137/18M1170194.

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.

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.

SEDLÁČKOVÁ, Jitka and Edit H. KONTRA. Foreign Language Learning Experiences of Deaf and Severely Hard-of-Hearing Czech University Students. Pedagogická orientace. Česká pedagogická společnost o.s., 2019, vol. 29, No 3, p. 336-358. ISSN 1211-4669.

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.

ZESSIN, M., Z. KUTIL, M. MELESHIN, Z. NOVAKOVA, E. GHAZY, D. KALBAS, Martin MAREK, C. ROMIER, W. SIPPL, C. BARINKA and M. SCHUTKOWSKI. One-Atom Substitution Enables Direct and Continuous Monitoring of Histone Deacylase Activity. Biochemistry. Washington: American Chemical Society, 2019, vol. 58, No 48, p. 4777-4789. ISSN 0006-2960. Available from: https://dx.doi.org/10.1021/acs.biochem.9b00786.

VONÁSEK, Vojtěch, Adam JURČÍK, Katarína FURMANOVÁ and Barbora KOZLÍKOVÁ. Sampling-based Motion Planning for Tracking Evolution of Dynamic Tunnels in Molecular Dynamics Simulations. Journal of Intelligent & Robotic Systems. 2019, vol. 93, 3-4, p. 763-785. ISSN 0921-0296. Available from: https://dx.doi.org/10.1007/s10846-018-0877-6.

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.

SIMOBEN, Conrad V., Dina ROBAA, Alokta CHAKRABARTI, Karin SCHMIDTKUNZ, Martin MAREK, Julien LANCELOT, Srinivasaraghavan KANNAN, Jelena MELESINA, Tajith B. SHAIK, Raymond J. PIERCE, Christophe ROMIER, Manfred JUNG and Wolfgang SIPPL. A Novel Class of Schistosoma mansoni Histone Deacetylase 8 (HDAC8) Inhibitors Identified by Structure-Based Virtual Screening and In Vitro Testing. Molecules. BASEL: Mayer und Muller, 2018, vol. 23, No 3, p. 1-14. ISSN 1420-3049. Available from: https://dx.doi.org/10.3390/molecules23030566.

TÓTHOVÁ, Lenka and Jitka SEDLÁČKOVÁ. Academic mobilities of students with hearing impairment: Welcoming the challenges with specialized online course of written English. In 14th ESSE Conference. 2018.

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.

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.

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.

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.

MAREK, Martin, Tajith B. SHAIK, Tino HEIMBURG, Alokta CHAKRABARTI, Julien LANCELOT, Elizabeth RAMOS-MORALES, Cyrielle DA VEIGA, Dmitrii KALININ, Jelena MELESINA, Dina ROBAA, Karin SCHMIDTKUNZ, Takayoshi SUZUKI, Ralph HOLL, Eric ENNIFAR, Raymond J. PIERCE, Manfred JUNG, Wolfgang SIPPL and Christophe ROMIER. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. Journal of Medicinal Chemistry. Washington: American Chemical Society, 2018, vol. 61, No 22, p. 10000-10016. ISSN 0022-2623. Available from: https://dx.doi.org/10.1021/acs.jmedchem.8b01087.

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.

LECOINTRE, Bertrand, Remy NAROZNY, Maria Teresa BORRELLO, Johanna SENGER, Alokta CHAKRABARTI, Manfred JUNG, Martin MAREK, Christophe ROMIER, Jelena MELESINA, Wolfgang SIPPL, Laurent BISCHOFF and A. GANESAN. Isoform-selective HDAC1/16/8 inhibitors with an imidazo-ketopiperazine cap containing stereochemical diversity. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. LONDON: ROYAL SOC, 2018, vol. 373, No 1748, p. 1-7. ISSN 0962-8436. Available from: https://dx.doi.org/10.1098/rstb.2017.0364.

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.

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.

CHAMONIKOLASOVÁ, Jana, Ivona SCHÖFROVÁ, Jiří RAMBOUSEK, Kateřina BLAŽKOVÁ, Michael Matthew KAYLOR, Filip KRAJNÍK, Jiří LUKL, Jana PELCLOVÁ, Jitka SEDLÁČKOVÁ and Thomas Donaldson SPARLING. 14th ESSE Conference. 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.

MOSKALÍKOVÁ, Hana, Markéta KOTLÁNOVÁ, Zbyněk PROKOP and Veronika ŠTĚPÁNKOVÁ. Biosensorická špička s DgpA pro detekci v nízké teplotě 10 oC (The biosensor tip with DgpA for detection at low temperature, 10°C). 2017.

MOSKALÍKOVÁ, Hana, Markéta KOTLÁNOVÁ, Zbyněk PROKOP and Jaroslav ŘEZÁČ. Biosensorická špička s DhmeA pro detekci v alkalických podmínkách pH 10 (The biosensor tip for detection of halogenated pollutants (eg 1,2-dibromoethane) in the alkaline conditions, pH 10.). 2017.

MOSKALÍKOVÁ, Hana, Markéta KOTLÁNOVÁ, Zbyněk PROKOP and Jaroslav ŘEZÁČ. Biosensorická špička s LinA a LinB pro detekci beta-HCH (The biosensor tip with LinA and LinB for detection beta-HCH). 2017.

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.

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.

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.

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.

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.

FARKA, Zdeněk, Tomáš JUŘÍK, Matěj PASTUCHA, David KOVÁŘ and Petr SKLÁDAL. Immunosensors for detection of pathogenic bacteria. In From structures to optical functions: Layered materials serving biosensing. 2017.

SEDLÁČKOVÁ, Jitka. Individuální rozdíly v učení se cizím jazykům: specifická situace neslyšících (Individual differences in foreign language learning: the specific situation of the deaf). Komenský. Masarykova univerzita, 2017, vol. 141, No 3, p. 38-42. ISSN 0323-0449.

FURMANOVÁ, Katarína, Miroslava JAREŠOVÁ, Jan BYŠKA, Adam JURČÍK, Julius PARULEK, Helwig HAUSER and Barbora KOZLÍKOVÁ. Interactive Exploration of Ligand Transportation through Protein Tunnels. BMC Bioinformatics. BioMed Central, 2017, vol. 18, No 22, p. 1-16. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-016-1448-0.

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.

FARKA, Zdeněk, Tomáš JUŘÍK, David KOVÁŘ, Libuše TRNKOVÁ and Petr SKLÁDAL. Nanoparticle-Based Immunochemical Biosensors and Assays: Recent Advances and Challenges. Chemical Reviews. Washington, D.C., USA: American Chemical Society, 2017, vol. 117, No 15, p. 9973-10042. ISSN 0009-2665. Available from: https://dx.doi.org/10.1021/acs.chemrev.7b00037.

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.

KOVÁŘ, David, Aneta MALÁ, Jitka VAŇÁČKOVÁ, Michal KALINA, Zdenka FOHLEROVÁ, Antonín HLAVÁČEK, Zdeněk FARKA, Petr SKLÁDAL, Zenon STARČUK, Radovan JIŘÍK, Ondřej SLABÝ and Jaromír HUBÁLEK. Preparation and Characterisation of Highly Stable Iron Oxide Nanoparticles for Magnetic Resonance Imaging. Journal of Nanomaterials. London: Hindawi Publishing Corporation, 2017, vol. 2017, neuvedeno, p. nestránkováno, 8 pp. ISSN 1687-4110. Available from: https://dx.doi.org/10.1155/2017/7859289.

VALUCHOVÁ, Soňa, Jaroslav FULNEČEK, Zbyněk PROKOP, Peggy STOLT-BERGNER, Eliška JANOUŠKOVÁ, Ctirad HOFR and Karel ŘÍHA. Protection of Arabidopsis Blunt-Ended Telomeres Is Mediated by a Physical Association with the Ku Heterodimer. Plant Cell. ROCKVILLE: AMER SOC PLANT BIOLOGISTS, 2017, vol. 29, No 6, p. 1533-1545. ISSN 1040-4651. Available from: https://dx.doi.org/10.1105/tpc.17.00064.

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.

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.

JURČÍK, Adam, Julius PARULEK, Jiří SOCHOR and Barbora KOZLÍKOVÁ. Accelerated Visualization of Transparent Molecular Surfaces in Molecular Dynamics. In IEEE Pacific Visualization Symposium 2016. Taipei, Taiwan: IEEE, 2016, p. 112-119. ISBN 978-1-5090-1451-4. Available from: https://dx.doi.org/10.1109/PACIFICVIS.2016.7465258.

PROKOP, Zbyněk, Anežka NEČASOVÁ, Jana KLÁNOVÁ and Pavel ČUPR. Bioavailability and mobility of organic contaminants in soil: new three-step ecotoxicological evaluation. Environmental Science and Pollution Research. HEIDELBERG (GERMANY): SPRINGER HEIDELBERG, 2016, vol. 23, No 5, p. 4312-4319. ISSN 0944-1344. Available from: https://dx.doi.org/10.1007/s11356-015-5555-7.

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.

FARKA, Zdeněk, Tomáš JUŘÍK, Pavel PODEŠVA, David KOVÁŘ, František FORET and Petr SKLÁDAL. Gelatin-templated Nanostructured Gold for Electrochemical Detection of Glucose in Serum. In 67th Annual Meeting of the International Society of Electrochemistry. 2016.

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.

FARKA, Zdeněk, David KOVÁŘ, Tomáš JUŘÍK and Petr SKLÁDAL. Imunosensory pro rychlou detekci patogenních mikroorganismů. In XVI. mezioborové setkání mladých biologů, biochemiků a chemiků. 2016. ISSN 2336-7202.

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

FARKA, Zdeněk, Tomáš JUŘÍK, Matěj PASTUCHA, David KOVÁŘ, Karel LACINA and Petr SKLÁDAL. Rapid Immunosensing of Salmonella Typhimurium Using Electrochemical Impedance Spectroscopy: the Effect of Sample Treatment. Electroanalysis. Weinheim: Wiley, 2016, vol. 28, No 8, p. 1803-1809. ISSN 1040-0397. Available from: https://dx.doi.org/10.1002/elan.201600093.

GROSS, J., Zbyněk PROKOP, D. JANSSEN, Kurt FABER and M. HALL. Regio- and Enantioselective Sequential Dehalogenation of rac-1,3-Dibromobutane by Haloalkane Dehalogenase LinB. CHEMBIOCHEM. WILEY-V C H VERLAG GMBH, 2016, vol. 17, No 15, p. 1437-1441. ISSN 1439-4227. Available from: https://dx.doi.org/10.1002/cbic.201600227.

GLOSER, Vít, Halyna KOROVETSKA, Ana Isabel Martín VERTEDOR, Martina HÁJÍČKOVÁ, Zbyněk PROKOP, Sally WILKINSON and William DAVIES. The Dynamics of Xylem Sap pH under Drought: a Universal Response in Herbs? PLANT AND SOIL. Springer, 2016, vol. 409, 1-2, p. 259-272. ISSN 0032-079X. Available from: https://dx.doi.org/10.1007/s11104-016-2962-6.

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.

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.

POLACH, Petr and Zbyněk PROKOP. Firmware k ovládání biosensoru (Firmware for controlling the biosensor). 2015.

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.

SHRIVASTAVA, Nidhi, Zbyněk PROKOP and Ashwani KUMAR. Novel LinA Type 3 delta-Hexachlorocyclohexane Dehydrochlorinase. Applied and Environmental Microbiology. WASHINGTON, DC (USA): AMER SOC MICROBIOLOGY, 2015, vol. 81, No 21, p. 7553-7559. ISSN 0099-2240. Available from: https://dx.doi.org/10.1128/AEM.01683-15.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

LITERÁKOVÁ, Petra, Jan LOCHMAN, Zbyněk ZDRÁHAL, Zbyněk PROKOP, Vladimír MIKEŠ and Tomáš KAŠPAROVSKÝ. Determination of capsidiol in tobacco cells culture by HPLC. Journal of Chromatographic Science. 2010, vol. 48, No 6, p. 436-440. ISSN 0021-9665.

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.

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.

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.

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.

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.

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.

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.

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.

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

TVRZOVÁ, Ludmila, Jiří NEČA, Zbyněk ZDRÁHAL, Danuška HORÁKOVÁ, Miroslav NĚMEC and Zbyněk PROKOP. Degradation of 4 Nitroguaiacol and Other Nitroaromatic Compounds by Strains of Arthrobacter nitroguajacolicus. Archives of Microbiology. 2008, vol. 00, No 00, p. 00-00, 10 pp. ISSN 0302-8933.

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.

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.

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.

DVOŘÁK, Pavel, Martina PAVLOVÁ, Martin KLVAŇA, Zbyněk PROKOP and Yuji NAGATA. Semi-Rational Engineering of Haloalkane Dehalogenases DHAA Towards Improved Activity with 1,2-Dichloroethane. In XII. Working Meeting of Biochemists and Molecular Biologists. 2008.

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.

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.

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.

TVRZOVÁ, Ludmila, Jiří NEČA, Zbyněk ZDRÁHAL, Danuška HORÁKOVÁ, Miroslav NĚMEC and Zbyněk PROKOP. Degradation of 4 Nitroguaiacol and Other Nitroaromatic Compounds by Strains of Arthrobacter nitroguajacolicus. Archives of Microbiology. 2007, vol. 00, No 00, p. 00-00, 10 pp. 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.

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.

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.

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.

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.

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.

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.

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.

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.

TVRZOVÁ, Ludmila, Zbyněk PROKOP, Jitka NAVRÁTILOVÁ, Radka MULLEROVÁ and Jiří NEČA. Development of a microtiter plate-based method for determination of degradation profile of nitrophenolic compounds. Journal of Microbiological Methods. Amsterdam: Elsevier Science B.V., 2006, vol. 65, No 3, p. 551-556. ISSN 0167-7012.

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, 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, 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.

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.

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.

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.

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.

MONINCOVÁ, Marta, Yukari SATO, Iva TĚŠÍNSKÁ, Zbyněk PROKOP, Yuji NAGATA and Jiri DAMBORSKY. Substrátová specifita haloalkandehalogenáz (Substrate specificity of haloalkane dehalogenases). In Sborník abstraktů, STUDENTSKÁ VĚDECKÁ KONFERENCE v oboru chemie a biochemie. 1st ed. Brno: Přírodovědecká fakulta Masarykovy univerzity v Brně, 2004, p. 40.

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.

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.

PROKOP, Zbyněk, Pavel ČUPR, V. ZLEVOROVÁ-ZLÁMALÍKOVÁ, Josef KOMÁREK, Ladislav DUŠEK and Ivan HOLOUBEK. Mobility, bioavailability and toxic effects of cadmium in soil samples. Environmental Research. 2003, vol. 91, -, p. 119-126. ISSN 0013-9351.

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.

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.

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.

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.

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.

ÄŚUPR, Pavel, ZbynÄ›k PROKOP, Alan GAVEL, Alena ANSORGOVá and I HOLOUBEK. Bioavailability and mobility of organic contaminants in soil and sediment samples: a three-step ecotoxicology evaluation. In 6th SECOTOX World Conagress and 6th European Conference on Ecotoxicology and Environmental Safety. Krakow : Art-Tekst, 2001, p. 253. ISBN 83-88316-10-9.

PROKOP, Zbyněk and Ivan HOLOUBEK. The use of a microbial contact toxicity test for evaluating cadmium bioavailability in soil. J. Soils and Sediments. 2001, vol. 1, No 1, p. 21-24.

PROKOP, Zbyněk, Pavel ČUPR and Ivan HOLOUBEK. Hodnocení biodostupnosti organických látek půdním mikroorganismům kontaktními testy toxicity (Evaluation of bioassassment to soil microorganisms by contact toxicity tests). In Hodnocení rizik pro životní prostředí - ERA 2000. Brno: Masarykova univerzita & TOCOEN, s.r.o., 2000, p. 188-189. ISBN 80-210-2328-7.

ČUPR, Pavel, Zbyněk PROKOP, Michal ŠKAREK, Alan GAVEL, Blahoslav MARŠÁLEK, Karel CHROUST and Ivan HOLOUBEK. Screeningové hodnocení environmentálních rizik v sedimentech regionu Zlín (Screening assessment of environmental risks in Zlín region). In Hodnocení rizik pro životní prostředí - ERA 2000. Brno: Masarykova univerzita & TOCOEN, s.r.o., 2000, p. 174-176. ISBN 80-210-2328-7.