Jirí Damborský

51 papers A* 2Misc 1Journal 46Unranked 2

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Anticipating protein evolution with successor sequence predictor. J. Cheminformatics Rayyan T. Khan, Pavel Kohout, Milos Musil, Monika Rosinska, Jirí Damborský, Stanislav Mazurenko, David Bednar
2025	J	`jnl`	Decoding Protein Stabilization: Impact on Aggregation, Solubility, and Unfolding Mechanisms. J. Chem. Inf. Model. Martin Havlásek, Sérgio M. Marques, Veronika Szotkowska, Antonin Kunka, Petra Babková, Jirí Damborský, Zbynek Prokop, David Bednár
2025	A*	`conf`	Learning to engineer protein flexibility. ICLR Petr Kouba, Joan Planas-Iglesias, Jirí Damborský, Jirí Sedlár, Stanislav Mazurenko, Josef Sivic
2025	J	`jnl`	Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands. J. Cheminformatics Radek Halfar, Jirí Damborský, Sérgio M. Marques, Jan Martinovic
2024	J	`jnl`	A computational workflow for analysis of missense mutations in precision oncology. J. Cheminformatics 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
2024	J	`jnl`	BenchStab: a tool for automated querying of web-based stability predictors. Bioinform. Jan Velecký, Matej Berezný, Milos Musil, Jirí Damborský, David Bednar, Stanislav Mazurenko
2024	J	`jnl`	FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. Briefings Bioinform. Milos Musil, Andrej Jezik, Jana Horackova, Simeon Borko, Petr Kabourek, Jirí Damborský, David Bednar
2024	J	`jnl`	Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes. J. Cheminformatics Ondrej Vavra, Jonathan D. Tyzack, Farzan Haddadi, Jan Stourac, Jirí Damborský, Stanislav Mazurenko, Janet M. Thornton, David Bednar
2024	A*	`conf`	Learning to design protein-protein interactions with enhanced generalization. ICLR Anton Bushuiev, Roman Bushuiev, Petr Kouba, Anatolii Filkin, Marketa Gabrielova, Michal Gabriel, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic
2024	J	`jnl`	PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. Briefings Bioinform. 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
2024	J	`jnl`	Revealing data leakage in protein interaction benchmarks. CoRR Anton Bushuiev, Roman Bushuiev, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic
2023	J	`jnl`	Learning to design protein-protein interactions with enhanced generalization. CoRR Anton Bushuiev, Roman Bushuiev, Anatolii Filkin, Petr Kouba, Marketa Gabrielova, Michal Gabriel, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic
2023	J	`jnl`	pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. Bioinform. Ondrej Vavra, Jakub Beránek, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar
2022	J	`jnl`	CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. Nucleic Acids Res. Antonin Kunka, David Lacko, Jan Stourac, Jirí Damborský, Zbynek Prokop, Stanislav Mazurenko
2022	J	`jnl`	LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic Acids Res. 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
2022	J	`jnl`	PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 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
2021	J	`jnl`	FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction. Briefings Bioinform. Milos Musil, Rayyan T. Khan, Andy Beier, Jan Stourac, Hannes Konegger, Jirí Damborský, David Bednar
2021	J	`jnl`	FireProtDB: database of manually curated protein stability data. Nucleic Acids Res. Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jirí Damborský, Stanislav Mazurenko, David Bednar
2021	J	`jnl`	SoluProt: prediction of soluble protein expression in Escherichia coli. Bioinform. Jirí Hon, Martin Marusiak, Tomás Martínek, Antonin Kunka, Jaroslav Zendulka, David Bednar, Jirí Damborský
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
2020	J	`jnl`	DockVis: Visual Analysis of Molecular Docking Trajectories. Comput. Graph. Forum Katarína Furmanová, Ondrej Vávra, Barbora Kozlíková, Jirí Damborský, Vojtech Vonásek, David Bednar, Jan Byska
2020	J	`jnl`	EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. Nucleic Acids Res. Jirí Hon, Simeon Borko, Jan Stourac, Zbynek Prokop, Jaroslav Zendulka, David Bednar, Tomás Martínek, Jirí Damborský
2019	J	`jnl`	Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Comput. Graph. Forum Jan Byska, Thomas Trautner, Sérgio M. Marques, Jirí Damborský, Barbora Kozlíková, Manuela Waldner
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
2018	J	`jnl`	CalFitter: a web server for analysis of protein thermal denaturation data. Nucleic Acids Res. Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljkovic, David Bednar, Zbynek Prokop, Jirí Damborský
2018	J	`jnl`	Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips. Sensors Zdenek Pilát, Martin Kizovský, Jan Jezek, Stanislav Krátký, Jaroslav Sobota, Martin Siler, Ota Samek, Tomas Buryska, Pavel Vanácek, Jirí Damborský, Zbynek Prokop, Pavel Zemánek
2018	J	`jnl`	HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. Nucleic Acids Res. Lenka Sumbalova, Jan Stourac, Tomás Martínek, David Bednar, Jirí Damborský
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
2017	Misc	`conf`	Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets. PACBB Stanislav Mazurenko, Jirí Damborský, Zbynek Prokop
2017	—	`conf`	Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. VCBM Viktor Vad, Jan Byska, Adam Jurcík, Ivan Viola, M. Eduard Gröller, Helwig Hauser, Sérgio M. Marques, Jirí Damborský, Barbora Kozlíková
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
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
2011	—	`conf`	CETOCOEN Project: From the Laboratory to the Field and Beyond. ISESS Jana Klánová, Ludek Bláha, Jirí Damborský, Petr Klán, Ladislav Dusek, Ivan Holoubek
2009	J	`jnl`	HotSpot Wizard: a web server for identification of hot spots in protein engineering. Nucleic Acids Res. Antonín Pavelka, Eva Chovancová, Jirí Damborský
2006	J	`jnl`	CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinform. Martin Petrek, Michal Otyepka, Pavel Banás, Pavlína Kosinová, Jaroslav Koca, Jirí Damborský
2006	J	`jnl`	Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. J. Comput. Aided Mol. Des. Pavel Banás, Michal Otyepka, Petr Jerábek, Martin Petrek, Jirí Damborský
2004	J	`jnl`	Binding of Fatty Acids to beta-Cryptogein: Quantitative Structure-Activity Relationships and Design of Selective Protein Mutants. J. Chem. Inf. Model. Petr Dobes, Jan Kmunícek, Vladimír Mikes, Jirí Damborský
2003	J	`jnl`	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. Jan Kmunícek, Michal Bohác, Santos Luengo, Federico Gago, Rebecca C. Wade, Jirí Damborský
2000	J	`jnl`	Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. Michal Cajan, Jirí Damborský, Ivan Stibor, Jaroslav Koca
2000	J	`jnl`	TRITON: in silico construction of protein mutants and prediction of their activities. Bioinform. Martin Prokop, Jirí Damborský, Jaroslav Koca
1998	J	`jnl`	A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism. J. Chem. Inf. Comput. Sci. Michal Kutý, Jirí Damborský, Martin Prokop, Jaroslav Koca
1997	J	`jnl`	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. Jirí Damborský, Michal Kutý, Miroslav Nemec, Jaroslav Koca