Jirí Damborský

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 29

Top Topics

Molecular Dynamics

Geographical Regions

Protein Structure

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Anton Bushuiev, Roman Bushuiev, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic
Revealing data leakage in protein interaction benchmarks. CoRR (2024)
Anton Bushuiev, Roman Bushuiev, Petr Kouba, Anatolii Filkin, Marketa Gabrielova, Michal Gabriel, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic
Learning to design protein-protein interactions with enhanced generalization. ICLR (2024)
Rayyan T. Khan, Petra Pokorna, Jan Stourac, Simeon Borko, Ihor Arefiev, Joan Planas-Iglesias, Adam Dobias, Gaspar R. P. Pinto, Veronika Szotkowska, Jaroslav Sterba, Ondrej Slaby, Jirí Damborský, Stanislav Mazurenko, David Bednar
A computational workflow for analysis of missense mutations in precision oncology. J. Cheminformatics 16 (1) (2024)
Jan Stourac, Simeon Borko, Rayyan T. Khan, Petra Pokorna, Adam Dobias, Joan Planas-Iglesias, Stanislav Mazurenko, Gaspar R. P. Pinto, Veronika Szotkowska, Jaroslav Sterba, Ondrej Slaby, Jirí Damborský, David Bednar
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. Briefings Bioinform. 25 (1) (2023)
Anton Bushuiev, Roman Bushuiev, Anatolii Filkin, Petr Kouba, Marketa Gabrielova, Michal Gabriel, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic
Learning to design protein-protein interactions with enhanced generalization. CoRR (2023)
Ondrej Vavra, Jakub Beránek, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar
pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. Bioinform. 39 (8) (2023)
Milos Musil, Andrej Jezik, Jana Horackova, Simeon Borko, Petr Kabourek, Jirí Damborský, David Bednar
FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. Briefings Bioinform. 25 (1) (2023)
Joan Planas-Iglesias, Filip Opálený, Pavol Ulbrich, Jan Stourac, Zainab K. Sanusi, Gaspar R. P. Pinto, Andrea Schenkmayerova, Jan Byska, Jirí Damborský, Barbora Kozlíková, David Bednar
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic Acids Res. 50 (W1) (2022)
Mihaly Varadi, Stephen Anyango, David R. Armstrong, John M. Berrisford, Preeti Choudhary, Mandar S. Deshpande, Nurul Nadzirin, Sreenath Nair, Lukás Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo 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, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50 (D1) (2022)
Antonin Kunka, David Lacko, Jan Stourac, Jirí Damborský, Zbynek Prokop, Stanislav Mazurenko
CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. Nucleic Acids Res. 50 (W1) (2022)
Jirí Hon, Martin Marusiak, Tomás Martínek, Antonin Kunka, Jaroslav Zendulka, David Bednar, Jirí Damborský
SoluProt: prediction of soluble protein expression in Escherichia coli. Bioinform. 37 (1) (2021)
Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jirí Damborský, Stanislav Mazurenko, David Bednar
FireProtDB: database of manually curated protein stability data. Nucleic Acids Res. 49 (Database-Issue) (2021)
Katarína Furmanová, Ondrej Vávra, Barbora Kozlíková, Jirí Damborský, Vojtech Vonásek, David Bednar, Jan Byska
DockVis: Visual Analysis of Molecular Docking Trajectories. Comput. Graph. Forum 39 (6) (2020)
Jirí Hon, Simeon Borko, Jan Stourac, Zbynek Prokop, Jaroslav Zendulka, David Bednar, Tomás Martínek, Jirí Damborský
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Jiri Filipovic, Ondrej Vávra, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Ludek Matyska, Jirí Damborský
CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (5) (2020)
Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Jan Stourac, Ludek Matyska, Jirí Damborský
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinform. 35 (23) (2019)
Jan Byska, Thomas Trautner, Sérgio M. Marques, Jirí Damborský, Barbora Kozlíková, Manuela Waldner
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Comput. Graph. Forum 38 (3) (2019)
Jan Stourac, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar R. P. Pinto, Jan Brezovsky, Jirí Damborský, David Bednar
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljkovic, David Bednar, Zbynek Prokop, Jirí Damborský
CalFitter: a web server for analysis of protein thermal denaturation data. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Lenka Sumbalova, Jan Stourac, Tomás Martínek, David Bednar, Jirí Damborský
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Zdenek Pilát, Martin Kizovský, Jan Jezek, Stanislav Krátký, Jaroslav Sobota, Martin Siler, Ota Samek, Tomas Buryska, Pavel Vanácek, Jirí Damborský, Zbynek Prokop, Pavel Zemánek
Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips. Sensors 18 (10) (2018)
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
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories. Bioinform. 34 (20) (2018)
Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomás Martínek, David Bednar, Jirí Damborský
FireProt: web server for automated design of thermostable proteins. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Sérgio M. Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jirí Damborský
Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling. J. Chem. Inf. Model. 57 (8) (2017)
Stanislav Mazurenko, Jirí Damborský, Zbynek Prokop
Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets. PACBB (2017)
Viktor Vad, Jan Byska, Adam Jurcík, Ivan Viola, M. Eduard Gröller, Helwig Hauser, Sérgio M. Marques, Jirí Damborský, Barbora Kozlíková
Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. VCBM (2017)
Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jan Brezovsky, Jirí Damborský
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Jaroslav Bendl, Milos Musil, Jan Stourac, Jaroslav Zendulka, Jirí Damborský, Jan Brezovsky
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. PLoS Comput. Biol. 12 (5) (2016)
Antonín Pavelka, Eva Sebestova, Barbora Kozlíková, Jan Brezovsky, Jirí Sochor, Jirí Damborský
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (3) (2016)
Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jirí Damborský, Jan Brezovsky
Screening. J. Chem. Inf. Model. 55 (1) (2015)
David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLoS Comput. Biol. 11 (11) (2015)
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
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. Bioinform. 30 (18) (2014)
Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonín Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jirí Damborský
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations. PLoS Comput. Biol. 10 (1) (2014)
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
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Comput. Biol. 8 (10) (2012)
Jana Klánová, Ludek Bláha, Jirí Damborský, Petr Klán, Ladislav Dusek, Ivan Holoubek
CETOCOEN Project: From the Laboratory to the Field and Beyond. ISESS (2011)
Antonín Pavelka, Eva Chovancová, Jirí Damborský
HotSpot Wizard: a web server for identification of hot spots in protein engineering. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Pavel Banás, Michal Otyepka, Petr Jerábek, Martin Petrek, Jirí Damborský
Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. J. Comput. Aided Mol. Des. 20 (6) (2006)
Martin Petrek, Michal Otyepka, Pavel Banás, Pavlína Kosinová, Jaroslav Koca, Jirí Damborský
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinform. 7 (2006)
Petr Dobes, Jan Kmunícek, Vladimír Mikes, Jirí Damborský
Binding of Fatty Acids to beta-Cryptogein: Quantitative Structure-Activity Relationships and Design of Selective Protein Mutants. J. Chem. Inf. Model. 44 (6) (2004)
Jan Kmunícek, Michal Bohác, Santos Luengo, Federico Gago, Rebecca C. Wade, Jirí Damborský
Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. J. Comput. Aided Mol. Des. 17 (5-6) (2003)
Michal Cajan, Jirí Damborský, Ivan Stibor, Jaroslav Koca
Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. 40 (5) (2000)
Martin Prokop, Jirí Damborský, Jaroslav Koca
TRITON: in silico construction of protein mutants and prediction of their activities. Bioinform. 16 (9) (2000)
Michal Kutý, Jirí Damborský, Martin Prokop, Jaroslav Koca
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism. J. Chem. Inf. Comput. Sci. 38 (4) (1998)
Jirí Damborský, Michal Kutý, Miroslav Nemec, Jaroslav Koca
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 1. Quantum Chemical Study of the First Reaction Step. J. Chem. Inf. Comput. Sci. 37 (3) (1997)