Jirí Damborský

According to our database, Jirí Damborský authored at least 44 papers between 1997 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.

Ondrej Vavra, Jonathan D. Tyzack, Farzan Haddadi, Jan Stourac, Jirí Damborský, Stanislav Mazurenko, Janet M. Thornton, David Bednar

J. Cheminformatics, December, 2024

A computational workflow for analysis of missense mutations in precision oncology.

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

J. Cheminformatics, December, 2024

Revealing data leakage in protein interaction benchmarks.

Anton Bushuiev, Roman Bushuiev, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic

CoRR, 2024

Learning to design protein-protein interactions with enhanced generalization.

Anton Bushuiev, Roman Bushuiev, Petr Kouba, Anatolii Filkin, Marketa Gabrielova, Michal Gabriel, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic

Proceedings of the Twelfth International Conference on Learning Representations, 2024

2023

PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning.

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

Briefings Bioinform., November, 2023

FireProt 2.0: web-based platform for the fully automated design of thermostable proteins.

Milos Musil, Andrej Jezik, Jana Horackova, Simeon Borko, Petr Kabourek, Jirí Damborský, David Bednar

Briefings Bioinform., November, 2023

pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support.

Ondrej Vavra, Jakub Beránek, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar

Bioinform., August, 2023

2022

PDBe-KB: collaboratively defining the biological context of structural data.

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

Nucleic Acids Res., 2022

LoopGrafter: a web tool for transplanting dynamical loops for protein engineering.

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

Nucleic Acids Res., 2022

CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability.

Antonin Kunka, David Lacko, Jan Stourac, Jirí Damborský, Zbynek Prokop, Stanislav Mazurenko

Nucleic Acids Res., 2022

2021

FireProtDB: database of manually curated protein stability data.

Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jirí Damborský, Stanislav Mazurenko, David Bednar

Nucleic Acids Res., 2021

SoluProt: prediction of soluble protein expression in Escherichia coli.

Jirí Hon, Martin Marusiak, Tomás Martínek, Antonin Kunka, Jaroslav Zendulka, David Bednar, Jirí Damborský

Bioinform., 2021

2020

CaverDock: A Novel Method for the Fast Analysis of Ligand Transport.

Jiri Filipovic, Ondrej Vávra, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Ludek Matyska, Jirí Damborský

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities.

Jirí Hon, Simeon Borko, Jan Stourac, Zbynek Prokop, Jaroslav Zendulka, David Bednar, Tomás Martínek, Jirí Damborský

Nucleic Acids Res., 2020

DockVis: Visual Analysis of Molecular Docking Trajectories.

Katarína Furmanová, Ondrej Vávra, Barbora Kozlíková, Jirí Damborský, Vojtech Vonásek, David Bednar, Jan Byska

Comput. Graph. Forum, 2020

2019

Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport.

Jan Stourac, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar R. P. Pinto, Jan Brezovsky, Jirí Damborský, David Bednar

Nucleic Acids Res., 2019

Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization.

Jan Byska, Thomas Trautner, Sérgio M. Marques, Jirí Damborský, Barbora Kozlíková, Manuela Waldner

Comput. Graph. Forum, 2019

CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels.

Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Jan Stourac, Ludek Matyska, Jirí Damborský

Bioinform., 2019

2018

Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips.

Zdenek Pilát, Martin Kizovský, Jan Jezek, Stanislav Krátký, Jaroslav Sobota, Martin Siler, Ota Samek, Tomas Buryska, Pavel Vanácek, Jirí Damborský, Zbynek Prokop, Pavel Zemánek

Sensors, 2018

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.

Lenka Sumbalova, Jan Stourac, Tomás Martínek, David Bednar, Jirí Damborský

Nucleic Acids Res., 2018

CalFitter: a web server for analysis of protein thermal denaturation data.

Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljkovic, David Bednar, Zbynek Prokop, Jirí Damborský

Nucleic Acids Res., 2018

CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.

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

Bioinform., 2018

2017

Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling.

Sérgio M. Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jirí Damborský

J. Chem. Inf. Model., August, 2017

FireProt: web server for automated design of thermostable proteins.

Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomás Martínek, David Bednar, Jirí Damborský

Nucleic Acids Res., 2017

Watergate: Visual Exploration of Water Trajectories in Protein Dynamics.

Viktor Vad, Jan Byska, Adam Jurcík, Ivan Viola, M. Eduard Gröller, Helwig Hauser, Sérgio M. Marques, Jirí Damborský, Barbora Kozlíková

Proceedings of the VCBM 17: Eurographics Workshop on Visual Computing for Biology and Medicine, 2017

Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets.

Stanislav Mazurenko, Jirí Damborský, Zbynek Prokop

Proceedings of the 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017

2016

CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules.

Antonín Pavelka, Eva Sebestova, Barbora Kozlíková, Jan Brezovsky, Jirí Sochor, Jirí Damborský

IEEE ACM Trans. Comput. Biol. Bioinform., 2016

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.

Jaroslav Bendl, Milos Musil, Jan Stourac, Jaroslav Zendulka, Jirí Damborský, Jan Brezovsky

PLoS Comput. Biol., 2016

HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.

Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jan Brezovsky, Jirí Damborský

Nucleic Acids Res., 2016

2015

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.

David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský

PLoS Comput. Biol., 2015

Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using <i>in Silico</i> Screening.

Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jirí Damborský, Jan Brezovsky

J. Chem. Inf. Model., 2015

2014

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations.

Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonín Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jirí Damborský

PLoS Comput. Biol., 2014

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures.

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

Bioinform., 2014

2012

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures.

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

PLoS Comput. Biol., 2012

2011

CETOCOEN Project: From the Laboratory to the Field and Beyond.

Jana Klánová, Ludek Bláha, Jirí Damborský, Petr Klán, Ladislav Dusek, Ivan Holoubek

Proceedings of the Environmental Software Systems. Frameworks of eEnvironment, 2011

2009

HotSpot Wizard: a web server for identification of hot spots in protein engineering.

Antonín Pavelka, Eva Chovancová, Jirí Damborský

Nucleic Acids Res., 2009

2006

Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.

Pavel Banás, Michal Otyepka, Petr Jerábek, Martin Petrek, Jirí Damborský

J. Comput. Aided Mol. Des., 2006

CAVER: a new tool to explore routes from protein clefts, pockets and cavities.

Martin Petrek, Michal Otyepka, Pavel Banás, Pavlína Kosinová, Jaroslav Koca, Jirí Damborský

BMC Bioinform., 2006

2004

Binding of Fatty Acids to beta-Cryptogein: Quantitative Structure-Activity Relationships and Design of Selective Protein Mutants.

Petr Dobes, Jan Kmunícek, Vladimír Mikes, Jirí Damborský

J. Chem. Inf. Model., 2004

2003

Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations.

Jan Kmunícek, Michal Bohác, Santos Luengo, Federico Gago, Rebecca C. Wade, Jirí Damborský

J. Comput. Aided Mol. Des., 2003

2000

Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships.

Michal Cajan, Jirí Damborský, Ivan Stibor, Jaroslav Koca

J. Chem. Inf. Comput. Sci., 2000

TRITON: in silico construction of protein mutants and prediction of their activities.

Martin Prokop, Jirí Damborský, Jaroslav Koca

Bioinform., 2000

1998

A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism.

Michal Kutý, Jirí Damborský, Martin Prokop, Jaroslav Koca

J. Chem. Inf. Comput. Sci., 1998

1997

A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 1. Quantum Chemical Study of the First Reaction Step.

Jirí Damborský, Michal Kutý, Miroslav Nemec, Jaroslav Koca

J. Chem. Inf. Comput. Sci., 1997