Výpis publikací

MARQUES, Sérgio Manuel; Joan PLANAS IGLESIAS; Jan VELECKÝ; Miloš MUSIL; Yasuhisa ASANO; Tomasz BOROWSKI; Vania BRISSOS; Marco CESPUGLI; Koar CHOROZIAN; Mohammad DADASHIPOUR; Elif ERDEM; Erica Elisa FERRANDI; Konstantinos GRIGORAKIS; Anna KLUZA; Janina LAWNICZEK; Konstantinos MAKRYNIOTIS; Daniela MONTI; Bettina NESTL; Anna C. NGO; Efstratios NIKOLAIVITS; Stefania PATTI; Christina PENTARI; Carolina F. RODRIGUES; Tobias SCHOPPER; Karolina SEWERYN-OZOG; Maciej SZALENIEC; Andre TABORDA; Mateusz TATARUCH; Dirk TISCHLER; Evangelos TOPAKAS; Jingyu WANG; Patrycja WOJCIK; Agnieszka M. WOJTKIEWICZ; John M. WOODLEY; Olga ZASTAWNY; Ligia O. MARTINS; Marco FRAAIJE; Jurgen PLEISS; Santiago SCHNELL; Jiří DAMBORSKÝ; Stanislav MAZURENKO a David BEDNÁŘ. Mobilizing the Biocatalysis Community for Reproducible and Reusable Data Collection. ACS Catalysis. WASHINGTON: American Chemical Society, 2026, roč. 16, č. 10, s. 8858-8868. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.5c07904.

BERGER, Jonathan B.; Sérgio Manuel MARQUES; Julian L. WISSNER; Jona T. SCHELLE; Jules BEEKWILDER; Jiří DAMBORSKÝ a Bernhard HAUER. Regioselective Sesquiterpene Hydroxylation Directed by Tunnel Remodeling in Rieske Oxygenases. JACS Au. WASHINGTON: AMER CHEMICAL SOC, 2026, roč. 6, č. 2, s. 847-857. ISSN 2691-3704. Dostupné z: https://doi.org/10.1021/jacsau.5c01130.

FRANKO, Ondrej; Martina CIZMARIKOVA; Martin KELLO; Radka MICHALKOVA; Olga WESOLOWSKA; Kamila SRODA-POMIANEK; Sérgio Manuel MARQUES; David BEDNÁŘ; Viktoria HAZIKOVA; Tomas Jan LISKA a Viera HABALOVA. Acridine-Based Chalcone 1C and ABC Transporters. International Journal of Molecular Sciences. BASEL: Molecular Diversity Preservation International, 2025, roč. 26, č. 9, s. 1-27. ISSN 1661-6596. Dostupné z: https://doi.org/10.3390/ijms26094138.

MARQUES, Sérgio Manuel; Simeon BORKO; Ondřej VÁVRA; Jan DVORSKÝ; Pavel KOHOUT; Petr KABOUREK; Lukáš HEJTMÁNEK; Jiří DAMBORSKÝ a David BEDNÁŘ. Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins. Nucleic Acids Research. Oxford: Oxford University Press, 2025, roč. 53, W1, s. "W132"-"W142", 11 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkaf399.

HAVLÁSEK, Martin; Sérgio Manuel MARQUES; Veronika SZOTKOWSKÁ; Antonín KUNKA; Petra BABKOVÁ; Jiří DAMBORSKÝ; Zbyněk PROKOP a David BEDNÁŘ. Decoding Protein Stabilization: Impact on Aggregation, Solubility, and Unfolding Mechanisms. Journal of Chemical Information and Modeling. WASHINGTON: AMER CHEMICAL SOC, 2025, roč. 65, č. 16, s. 8688-8701. ISSN 1549-9596. Dostupné z: https://doi.org/10.1021/acs.jcim.5c00611.

HALFAR, Radek; Jiří DAMBORSKÝ; Sérgio Manuel MARQUES a Jan MARTINOVIC. Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2025, roč. 17, č. 1, s. 1-10. ISSN 1758-2946. Dostupné z: https://doi.org/10.1186/s13321-025-01005-4.

SLÁNSKÁ, Michaela; Lenka ŠTACKOVÁ; Sérgio Manuel MARQUES; Peter ŠTACKO; Marek MARTÍNEK; Luboš JÍLEK; Martin TOUL; Jiří DAMBORSKÝ; David BEDNÁŘ; Petr KLÁN a Zbyněk PROKOP. Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2024, roč. 14, č. 15, s. 11635-11645. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.4c03503.

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 a David BEDNÁŘ. CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS AU. WASHINGTON: AMER CHEMICAL SOC, 2024, roč. 4, č. 6, s. 2228-2245. ISSN 2691-3704. Dostupné z: https://doi.org/10.1021/jacsau.4c00182.

SLÁNSKÁ, Michaela; Lenka ŠTACKOVÁ; Sérgio Manuel MARQUES; P. ŠTACKO; Marek MARTÍNEK; Luboš JÍLEK; Martin TOUL; Jiří DAMBORSKÝ; David BEDNÁŘ; Petr KLÁN a Zbyněk PROKOP. Fotoaktivovatelný substrát na bázi azobenzenu pro halogenalkandehalogenázy. 2024.

PUSHKAROVA, Nadiia; Jana HENNELOVA; Sérgio Manuel MARQUES; David BEDNÁŘ; Kamil PARUCH; Naresh AKAVARAM; L. SPICHAL; Jiří DAMBORSKÝ; A. YEMETS a 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 a Michael KRONE. InVADo: Interactive Visual Analysis of Molecular Docking Data. IEEE Transactions on Visualization and Computer Graphics. IEEE Computer Society, 2024, roč. 30, č. 4, s. 1984-1997. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2023.3337642.

KUNKA, Antonín; Sérgio Manuel MARQUES; Martin HAVLÁSEK; Michal VAŠINA; Nikola VELÁTOVÁ; Lucia CENGELOVÁ; David KOVÁŘ; Jiří DAMBORSKÝ; Martin MAREK; David BEDNÁŘ a 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, roč. 13, č. 19, s. 12506-12518. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.3c02575.

ŠNAJDAROVÁ, Karolína; Sérgio Manuel MARQUES; Jiří DAMBORSKÝ; David BEDNÁŘ a 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, roč. 79, November, s. 956-970. ISSN 2059-7983. Dostupné z: https://doi.org/10.1107/S2059798323006642.

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 a 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, roč. 18, č. 1, s. 1-25. ISSN 1750-1326. Dostupné z: https://doi.org/10.1186/s13024-023-00620-9.

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 a Martin MAREK. Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nature Communications. Berlin: Nature, 2023, roč. 14, č. 1, s. 1-20. ISSN 2041-1723. Dostupné z: https://doi.org/10.1038/s41467-023-43403-y.

ULBRICH, Pavol; Manuela WALDNER; Katarína FURMANOVÁ; Sérgio Manuel MARQUES; David BEDNÁŘ; Barbora KOZLÍKOVÁ a Jan BYŠKA. sMolBoxes: Dataflow Model for Molecular Dynamics Exploration. IEEE Transactions on Visualization and Computer Graphics. United States: IEEE Computer Society, 2023, roč. 29, č. 1, s. 581-590. ISSN 1077-2626. Dostupné z: https://doi.org/10.1109/TVCG.2022.3209411.

RAPP, Lea R.; Sérgio Manuel MARQUES; Bernd NEBEL; Jiří DAMBORSKÝ a 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, roč. 14, č. 6, s. 1-5. ISSN 1867-3880. Dostupné z: https://doi.org/10.1002/cctc.202101648.

MARQUES, Sérgio Manuel; Michaela SLÁNSKÁ; Klaudia CHMELOVÁ; Radka CHALOUPKOVÁ; Martin MAREK; Spencer CLARK; Jiří DAMBORSKÝ; Eric T. KOOL; David BEDNÁŘ a Zbyněk PROKOP. Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling. JACS AU. WASHINGTON: AMER CHEMICAL SOC, 2022, roč. 2, č. 6, s. 1324-1337. ISSN 2691-3704. Dostupné z: https://doi.org/10.1021/jacsau.2c00002.

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

PLANAS IGLESIAS, Joan; Sérgio Manuel MARQUES; José Gaspar RANGEL PAMPLONA PIZARRO PINTO; Miloš MUSIL; Jan ŠTOURAČ; Jiří DAMBORSKÝ a David BEDNÁŘ. Computational design of enzymes for biotechnological applications. Biotechnology Advances. OXFORD: Elsevier, 2021, roč. 47, March–April, s. 1-22. ISSN 0734-9750. Dostupné z: https://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 a 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 a 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, roč. 11, č. 21, s. 12864-12885. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.1c03343.

MARQUES, Sérgio Manuel; Lucie ŠUPOLÍKOVÁ; Lenka MOLČANOVÁ; Karel ŠMEJKAL; David BEDNÁŘ a Iva SLANINOVÁ. Screening of Natural Compounds as P-Glycoprotein Inhibitors against Multidrug Resistance. BIOMEDICINES. BASEL: MDPI, 2021, roč. 9, č. 4, s. 1-22. ISSN 2227-9059. Dostupné z: https://doi.org/10.3390/biomedicines9040357.

RANGEL PAMPLONA PIZARRO PINTO, José Gaspar; Ondřej VÁVRA; Sérgio Manuel MARQUES; Jiří FILIPOVIČ; David BEDNÁŘ a 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, roč. 19, May, s. 3187-3197. ISSN 2001-0370. Dostupné z: https://doi.org/10.1016/j.csbj.2021.05.043.

RAPP, Lea R.; Sérgio Manuel MARQUES; Erna ZUKIC; Benjamin ROWLINSON; Mahima SHARMA; Gideon GROGAN; Jiří DAMBORSKÝ a 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, roč. 11, č. 5, s. 3182-3189. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.0c05193.

MARQUES, Sérgio Manuel; Joan PLANAS IGLESIAS a Jiří DAMBORSKÝ. Web-based tools for computational enzyme design. Current Opinion in Structural Biology. London: Elsevier Science Ltd., 2021, roč. 69, August 2021, s. 19-34. ISSN 0959-440X. Dostupné z: https://doi.org/10.1016/j.sbi.2021.01.010.

FILIPOVIČ, Jiří; Ondřej VÁVRA; Jan PLHÁK; David BEDNÁŘ; Sérgio Manuel MARQUES; Jan BREZOVSKÝ; Luděk MATYSKA a 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, roč. 17, č. 5, s. 1625-1638. ISSN 1545-5963. Dostupné z: https://doi.org/10.1109/TCBB.2019.2907492.

MARKOVÁ, Klára; Klaudia CHMELOVÁ; Sérgio Manuel MARQUES; Philippe CARPENTIER; David BEDNÁŘ; Jiří DAMBORSKÝ a Martin MAREK. Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chemical Science. Cambridge: Royal Society of Chemistry, 2020, roč. 11, č. 41, s. 11162-11178. ISSN 2041-6520. Dostupné z: https://doi.org/10.1039/d0sc03367g.

BYŠKA, Jan; Thomas TRAUTNER; Sérgio Manuel MARQUES; Jiří DAMBORSKÝ; Barbora KOZLÍKOVÁ a Manuela WALDNER. Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Computer Graphics Forum. Wiley-Blackwell, 2019, roč. 38, č. 3, s. 441-453. ISSN 0167-7055. Dostupné z: https://doi.org/10.1111/cgf.13701.

VÁVRA, Ondřej; Jiří FILIPOVIČ; Jan PLHÁK; David BEDNÁŘ; Sérgio Manuel MARQUES; Jan BREZOVSKÝ; Jan ŠTOURAČ; Luděk MATYSKA a Jiří DAMBORSKÝ. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics. Oxford: Oxford University Press, 2019, roč. 35, č. 23, s. 4986-4993. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btz386.

MARQUES, Sérgio Manuel; David BEDNÁŘ a Jiří DAMBORSKÝ. Computational Study of Protein-Ligand Unbinding for Enzyme Engineering. FRONTIERS IN CHEMISTRY. LAUSANNE: FRONTIERS MEDIA SA, 2019, roč. 6, JAN 2019, s. 1-15. ISSN 2296-2646. Dostupné z: https://doi.org/10.3389/fchem.2018.00650.

CERNY, J.; P. BOZIKOVA; A. BALIK; Sérgio Manuel MARQUES a L. VYKLICKY. NMDA Receptor Opening and Closing-Transitions of a Molecular Machine Revealed by Molecular Dynamics. Biomolecules. BASEL: MDPI, 2019, roč. 9, č. 10, s. 1-17. ISSN 2218-273X. Dostupné z: https://doi.org/10.3390/biom9100546.

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 a Barbora KOZLÍKOVÁ. CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics. 2018, roč. 34, č. 20, s. 3586-3588. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/bty386.

BEERENS, Koen; Stanislav MAZURENKO; Antonín KUNKA; Sérgio Manuel MARQUES; N. HANSEN; Miloš MUSIL; Radka CHALOUPKOVÁ; Jitka WATERMAN; Jan BREZOVSKÝ; David BEDNÁŘ; Zbyněk PROKOP a Jiří DAMBORSKÝ. Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization. ACS Catalysis. WASHINGTON: AMER CHEMICAL SOC, 2018, roč. 8, č. 10, s. 9420-9428. ISSN 2155-5435. Dostupné z: https://doi.org/10.1021/acscatal.8b01677.

KAUSHIK, Shubhangi; Sérgio Manuel MARQUES; Prashant Kumar KHIRSARIYA; Kamil PARUCH; Lenka LIBICHOVÁ; Jan BREZOVSKÝ; Zbyněk PROKOP; Radka CHALOUPKOVÁ a Jiří DAMBORSKÝ. Impact of the access tunnel engineering on catalysis is strictly ligand-specific. the FEBS Journal. 2018, roč. 285/2018, č. 8, s. 1456-1476. ISSN 1742-464X. Dostupné z: https://doi.org/10.1111/febs.14418.

MARQUES, Sérgio Manuel; Zuzana DUNAJOVÁ; Zbyněk PROKOP; Radka CHALOUPKOVÁ; Jan BREZOVSKÝ a 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, roč. 57, č. 8, s. 1970-1989. ISSN 1549-9596. Dostupné z: https://doi.org/10.1021/acs.jcim.7b00070.

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

MARQUES, Sérgio Manuel; Lukáš DANIEL; Tomáš BURYŠKA; Zbyněk PROKOP; Jan BREZOVSKÝ a Jiří DAMBORSKÝ. Enzyme Tunnels and Gates As Relevant Targets in Drug Design. MEDICINAL RESEARCH REVIEWS. Hoboken, USA: WILEY, 2017, roč. 37, č. 5, s. 1095-1139. ISSN 0198-6325. Dostupné z: https://doi.org/10.1002/med.21430.

VAD, Viktor; Jan BYŠKA; Adam JURČÍK; Ivan VIOLA; Eduard M. GRÖLLER; Helwig HAUSER; Sérgio Manuel MARQUES; Jiří DAMBORSKÝ a 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, s. 33-42. ISBN 978-3-03868-036-9.

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