Jan Brezovsky

20 papers Journal 20
YearRankTypeTitle / Venue / Authors
2025 J jnl
Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.
J. Chem. Inf. Model.
Aravind Selvaram Thirunavukarasu, Katarzyna Szleper, Gamze Tanriver, Igor Marchlewski, Karolina Mitusinska, Artur Góra, Jan Brezovsky
2024 J jnl
Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.
J. Chem. Inf. Model.
Nishita Mandal, Bartlomiej Surpeta, Jan Brezovsky
2024 J jnl
Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases.
J. Chem. Inf. Model.
Carlos Eduardo Sequeiros-Borja, Bartlomiej Surpeta, Aravind Selvaram Thirunavukarasu, Cedrix Jurgal Dongmo Foumthuim, Igor Marchlewski, Jan Brezovsky
2022 J jnl
TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them.
Bioinform.
Jan Brezovsky, Aravind Selvaram Thirunavukarasu, Bartlomiej Surpeta, Carlos Eduardo Sequeiros-Borja, Nishita Mandal, Dheeraj Kumar Sarkar, Cedrix Jurgal Dongmo Foumthuim, Nikhil Agrawal
2021 J jnl
Recent advances in user-friendly computational tools to engineer protein function.
Briefings Bioinform.
Carlos Eduardo Sequeiros-Borja, Bartlomiej Surpeta, Jan Brezovsky
2020 J jnl
CaverDock: A Novel Method for the Fast Analysis of Ligand Transport.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jiri Filipovic, Ondrej Vávra, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Ludek Matyska, Jirí Damborský
2019 J jnl
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport.
Nucleic Acids Res.
Jan Stourac, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar R. P. Pinto, Jan Brezovsky, Jirí Damborský, David Bednar
2019 J jnl
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels.
Bioinform.
Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Jan Stourac, Ludek Matyska, Jirí Damborský
2018 J jnl
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.
Bioinform.
Adam Jurcík, David Bednar, Jan Byska, Sérgio M. Marques, Katarína Furmanová, Lukas Daniel, Piia Kokkonen, Jan Brezovsky, Ondrej Strnad, Jan Stourac, Antonín Pavelka, Martin Manak, Jirí Damborský, Barbora Kozlíková
2017 J jnl
Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling.
J. Chem. Inf. Model.
Sérgio M. Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jirí Damborský
2017 J jnl
FireProt: web server for automated design of thermostable proteins.
Nucleic Acids Res.
Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomás Martínek, David Bednar, Jirí Damborský
2016 J jnl
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules.
IEEE ACM Trans. Comput. Biol. Bioinform.
Antonín Pavelka, Eva Sebestova, Barbora Kozlíková, Jan Brezovsky, Jirí Sochor, Jirí Damborský
2016 J jnl
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.
Nucleic Acids Res.
Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jan Brezovsky, Jirí Damborský
2016 J jnl
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
PLoS Comput. Biol.
Jaroslav Bendl, Milos Musil, Jan Stourac, Jaroslav Zendulka, Jirí Damborský, Jan Brezovsky
2016 J jnl
Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Res.
Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak
2015 J jnl
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.
PLoS Comput. Biol.
David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský
2015 J jnl
Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using
J. Chem. Inf. Model.
Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jirí Damborský, Jan Brezovsky
2014 J jnl
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.
Bioinform.
Barbora Kozlíková, Eva Sebestova, Vilém Sustr, Jan Brezovsky, Ondrej Strnad, Lukas Daniel, David Bednar, Antonín Pavelka, Martin Manak, Martin Bezdeka, Petr Benes, Matus Kotry, Artur Góra, Jirí Damborský, Jiri Sochor
2014 J jnl
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations.
PLoS Comput. Biol.
Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonín Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jirí Damborský
2012 J jnl
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures.
PLoS Comput. Biol.
Eva Chovancová, Antonín Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlíková, Artur Góra, Vilém Sustr, Martin Klvana, Petr Medek, Lada Biedermannová, Jiri Sochor, Jirí Damborský