Jan Brezovsky

According to our database, Jan Brezovsky authored at least 19 papers between 2012 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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

Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.

Nishita Mandal, Bartlomiej Surpeta, Jan Brezovsky

J. Chem. Inf. Model., 2024

2022

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

2021

Recent advances in user-friendly computational tools to engineer protein function.

Carlos Eduardo Sequeiros-Borja, Bartlomiej Surpeta, Jan Brezovsky

Briefings Bioinform., 2021

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

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 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

2018

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, Jirí Damborský, Barbora Kozlíková

Bioinform., 2018

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., August, 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

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

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

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, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak

Nucleic Acids Res., 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

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, Jirí Damborský

PLoS Comput. Biol., 2015

Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using <i>in Silico</i> Screening.

Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jirí Damborský, Jan Brezovsky

J. Chem. Inf. Model., 2015

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

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, Artur Góra, Jirí Damborský, Jiri Sochor

Bioinform., 2014

2012

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, Jirí Damborský

PLoS Comput. Biol., 2012