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)

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)

TRITON: in silico construction of protein mutants and prediction of their activities. - Martin Prokop; Jirí Damborský; Jaroslav Koca (Bioinform., 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)

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)

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)

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)

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)

HotSpot Wizard: a web server for identification of hot spots in protein engineering. - Antonín Pavelka; Eva Chovancová; Jirí Damborský (Nucleic Acids Res., 2009)

CETOCOEN Project: From the Laboratory to the Field and Beyond. - Jana Klánová; Ludek Bláha; Jirí Damborský; Petr Klán; Ladislav Dusek; Ivan Holoubek (ISESS, 2011)

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; et al. (PLoS Comput. Biol., 2012)

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; et al. (Bioinform., 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)

Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using in Silico Screening. - Lukas Daniel; Tomas Buryska; Zbynek Prokop; Jirí Damborský; Jan Brezovsky (J. Chem. Inf. Model., 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 001; Jirí Damborský (PLoS Comput. Biol., 2015)

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)

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)

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)

Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets. - Stanislav Mazurenko; Jirí Damborský; Zbynek Prokop (PACBB, 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 (VCBM, 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)

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., 2017)

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; et al. (Bioinform., 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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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; et al. (Nucleic Acids Res., 2022)

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., 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., 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; et al. (Briefings Bioinform., 2023)

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 (ICLR, 2024)

Revealing data leakage in protein interaction benchmarks. - Anton Bushuiev; Roman Bushuiev; Jirí Sedlár; Tomás Pluskal; Jirí Damborský; Stanislav Mazurenko; Josef Sivic (CoRR, 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; et al. (J. Cheminformatics, 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, 2024)

Learning to engineer protein flexibility. - Petr Kouba; Joan Planas-Iglesias; Jirí Damborský; Jirí Sedlár; Stanislav Mazurenko; Josef Sivic (ICLR, 2025)

Decoding Protein Stabilization: Impact on Aggregation, Solubility, and Unfolding Mechanisms. - Martin Havlásek; Sérgio M. Marques; Veronika Szotkowska; Antonin Kunka; Petra Babková; Jirí Damborský; Zbynek Prokop; David Bednár (J. Chem. Inf. Model., 2025)

Moldina: a fast and accurate search algorithm for simultaneous docking of multiple ligands. - Radek Halfar; Jirí Damborský; Sérgio M. Marques; Jan Martinovic (J. Cheminformatics, 2025)

Anticipating protein evolution with successor sequence predictor. - Rayyan T. Khan; Pavel Kohout; Milos Musil; Monika Rosinska; Jirí Damborský; Stanislav Mazurenko; David Bednar (J. Cheminformatics, 2025)