Flexible Cache for Database Management Systems. - Radim Baca; David Bednar (DATESO, 2011)

Index-based n-gram extraction from large document collections. - Michal Krátký; Radim Baca; David Bednar; Jirí Walder; Jiri Dvorský; Peter Chovanec (ICDIM, 2011)

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)

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)

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)

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)

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)

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)

PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization. - Javier L. Baylon; Oleg Ursu; Anja Muzdalo; Anne Mai Wassermann; Gregory L. Adams; Martin Spale; Petr Mejzlík; Anna Gromek; Viktor Pisarenko; Dzianis Hancharyk; Esteban Jenkins; David Bednar; et al. (J. Chem. Inf. Model., 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)

sMolBoxes: Dataflow Model for Molecular Dynamics Exploration. - Pavol Ulbrich; Manuela Waldner; Katarína Furmanová; Sérgio M. Marques; David Bednár; Barbora Kozlíková; Jan Byska (IEEE Trans. Vis. Comput. Graph., 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., 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)

InVADo: Interactive Visual Analysis of Molecular Docking Data. - Marco Schäfer; Nicolas Brich; Jan Byska; Sérgio M. Marques; David Bednár; Philipp Thiel; Barbora Kozlíková; Michael Krone (IEEE Trans. Vis. Comput. Graph., 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)

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)

Visual Support for the Loop Grafting Workflow on Proteins. - Filip Opálený; Pavol Ulbrich; Joan Planas-Iglesias; Jan Byska; Jan Stourac; David Bednár; Katarína Furmanová; Barbora Kozlíková (IEEE Trans. Vis. Comput. Graph., 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)