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)

Tools and data services registry: a community effort to document bioinformatics resources. - Jon C. Ison; Kristoffer Rapacki; Hervé Ménager; Matús Kalas; Emil Rydza; Piotr Chmura; Christian Anthon; Niall Beard; Karel Berka; Dan M. Bolser; Tim Booth; Anthony Bretaudeau; et al. (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)

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)

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)

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)

Recent advances in user-friendly computational tools to engineer protein function. - Carlos Eduardo Sequeiros-Borja; Bartlomiej Surpeta; Jan Brezovsky (Briefings Bioinform., 2021)

TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them. - Jan Brezovsky; Aravind Selvaram Thirunavukarasu; Bartlomiej Surpeta; Carlos Eduardo Sequeiros-Borja; Nishita Mandal; Dheeraj Kumar Sarkar; Cedrix Jurgal Dongmo Foumthuim; Nikhil Agrawal (Bioinform., 2022)

Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics. - Nishita Mandal; Bartlomiej Surpeta; Jan Brezovsky (J. Chem. Inf. Model., 2024)

Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases. - Carlos Eduardo Sequeiros-Borja; Bartlomiej Surpeta; Aravind Selvaram Thirunavukarasu; Cedrix Jurgal Dongmo Foumthuim; Igor Marchlewski; Jan Brezovsky (J. Chem. Inf. Model., 2024)

Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model. - Aravind Selvaram Thirunavukarasu; Katarzyna Szleper; Gamze Tanriver; Igor Marchlewski; Karolina Mitusinska; Artur Góra; Jan Brezovsky (J. Chem. Inf. Model., 2025)