Publications by authors named "Jan Brezovsky"

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Message hidden in α-helices-toward a better understanding of plant ABCG transporters' multispecificity.
Wanda Biała-Leonhard, Aleksandra Bigos, Jan Brezovsky, Michał Jasiński

Plant Physiol· April 2025

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Discovery of new inhibitors of nuclease MRE11.
Fedor Nikulenkov, Benoit Carbain, Raktim Biswas, Stepan Havel, Jana Prochazkova, Jan Brezovsky

Eur J Med Chem· March 2025

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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, Jan Brezovsky

J Chem Inf Model· January 2025

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Impact of water models on the structure and dynamics of enzyme tunnels.
Aaftaab Sethi, Nikhil Agrawal, Jan Brezovsky

Comput Struct Biotechnol J· December 2024

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Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases.
Carlos Sequeiros-Borja, Bartlomiej Surpeta, Aravind Selvaram Thirunavukarasu, Cedrix J Dongmo Foumthuim, Igor Marchlewski, Jan Brezovsky

J Chem Inf Model· August 2024

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Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics.
Nishita Mandal, Bartlomiej Surpeta, Jan Brezovsky

J Chem Inf Model· August 2024

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Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites.
Dheeraj Kumar Sarkar, Bartlomiej Surpeta, Jan Brezovsky

J Chem Theory Comput· July 2024

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Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters.
Konrad Pakuła, Carlos Sequeiros-Borja, Wanda Biała-Leonhard, Aleksandra Pawela, Joanna Banasiak, Jan Brezovsky

Cell Mol Life Sci· March 2023

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Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations.
Carlos Sequeiros-Borja, Bartlomiej Surpeta, Igor Marchlewski, Jan Brezovsky

MethodsX· December 2022

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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

Bioinformatics· March 2022

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CaverDock: A Novel Method for the Fast Analysis of Ligand Transport.
Jiri Filipovic, Ondrej Vavra, Jan Plhak, David Bednar, Sergio M Marques, Jan Brezovsky

IEEE/ACM Trans Comput Biol Bioinform· December 2021

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Recent advances in user-friendly computational tools to engineer protein function.
Carlos Eduardo Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovsky

Brief Bioinform· May 2021

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Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering.
Bartłomiej Surpeta, Carlos Eduardo Sequeiros-Borja, Jan Brezovsky

Int J Mol Sci· April 2020

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CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels.
Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sergio M Marques, Jan Brezovsky

Bioinformatics· December 2019

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Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium sp. ELB17.
Lukas Chrast, Katsiaryna Tratsiak, Joan Planas-Iglesias, Lukas Daniel, Tatyana Prudnikova, Jan Brezovsky

Microorganisms· October 2019

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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 Pinto, Jan Brezovsky

Nucleic Acids Res· July 2019

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Molecular Gating of an Engineered Enzyme Captured in Real Time.
Piia Kokkonen, Jan Sykora, Zbynek Prokop, Avisek Ghose, David Bednar, Jan Brezovsky

J Am Chem Soc· December 2018

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CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.
Adam Jurcik, David Bednar, Jan Byska, Sergio M Marques, Katarina Furmanova, Jan Brezovsky

Bioinformatics· October 2018

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Computational Analysis of Protein Tunnels and Channels.
Jan Brezovsky, Barbora Kozlikova, Jiri Damborsky

Methods Mol Biol· June 2018

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Computer-assisted engineering of hyperstable fibroblast growth factor 2.
Pavel Dvorak, David Bednar, Pavel Vanacek, Lukas Balek, Livia Eiselleova, Jan Brezovsky

Biotechnol Bioeng· April 2018

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Impact of the access tunnel engineering on catalysis is strictly ligand-specific.
Shubhangi Kaushik, Sérgio M Marques, Prashant Khirsariya, Kamil Paruch, Lenka Libichova, Jan Brezovsky

FEBS J· April 2018

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Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling.
Sérgio M Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky

J Chem Inf Model· August 2017

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Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity.
Petra Babkova, Eva Sebestova, Jan Brezovsky, Radka Chaloupkova, Jiri Damborsky

Chembiochem· July 2017

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FireProt: web server for automated design of thermostable proteins.
Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop

Nucleic Acids Res· July 2017

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Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear β-Haloalkanes: Open-Solvated versus Occluded-Desolvated Active Sites.
Veronika Liskova, Veronika Stepankova, David Bednar, Jan Brezovsky, Zbynek Prokop

Angew Chem Int Ed Engl· April 2017

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