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)

Top 10 metrics for life science software good practices. - Haydee Artaza; Neil P. Chue Hong; Manuel Corpas; Angel Corpuz; Rob W. W. Hooft; Rafael C. Jiménez; Brane Leskosek; Brett G. Olivier; Jan Stourac; Radka Svobodová Vareková; Thomas Van Parys; Daniel Vaughan (F1000Research, 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)

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)

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)

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)

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)

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)

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)

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)