Publication Records

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.

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

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

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

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

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

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

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.