All publications

Research groups

Laboratory of Cell Biology

Laboratory of Structural Biology

Laboratory of Bioinformatics and Protein Engineering

Laboratory of Molecular and Cellular Neurobiology

Laboratory of Neurodegeneration

Laboratory of Iron Homeostasis

Laboratory of Protein Structure

Laboratory of Protein Metabolism

Laboratory of Zebrafish Developmental Genomics

Laboratory of Biomolecular Interactions and Transport

Laboratory of RNA Biology - ERA Chairs Group

Laboratory of RNA-Protein Interactions - Dioscuri Centre

Laboratory of Prokaryotic Gene Regulation

Laboratory of Cellular Genomics

Laboratory of Cellular Proteostasis

Projects outside research groups

PolSenior Project

Aurezyna Project

Core Facilities

Core Facility

Zebrafish Core Facility

Former labs & projects

Department of Molecular Biology

Laboratory of Biomodelling

Laboratory of Cell Cortex Mechanisms

Laboratory of Mitochondrial Biogenesis

Cilia and leukemia genetics studies

Other

Other

2026 2025 2024 2023 2022 2021 2020 2018 2016

2026

Publication Unlocking High-Throughput Investigation of Transport Tunnels in Enzymes Using Coarse-Grained Simulation Methods. Mandal N, Stevens JA, Poma AB, Surpeta B, Sequeiros-Borja C, Thirunavukarasu AS, Marrink SJ, Brezovsky J. J Chem Theory Comput. 2026

2025

Publication Message hidden in α-helices-toward a better understanding of plant ABCG transporters' multispecificity. Biała-Leonhard W, Bigos A, Brezovsky J, Jasiński M. Plant Physiol. 2025 Publication Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model. Thirunavukarasu AS, Szleper K, Tanriver G, Marchlewski I, Mitusinska K, Gora A, Brezovsky J. J Chem Inf Model. 2025

2024

Publication Impact of water models on the structure and dynamics of enzyme tunnels. Sethi A, Agrawal N, Brezovsky J. Comput Struct Biotechnol J. 2024 Publication Suitability of Adenosine Derivatives in Improving the Activity and Stability of Cytochrome c under Stress: Insights into the Effect of Phosphate Groups. Bharadwaj P, Shet SM, Bisht M, Sarkar DK, Franklin G, Kotrappanavar NS, Mondal D. J Phys Chem B. 2024 Publication Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics. Mandal N, Surpeta B, Brezovsky J. J Chem Inf Model. 2024 Publication Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites. Sarkar DK, Surpeta B, Brezovsky J. J Chem Theory Comput. 2024 Publication Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases. Sequeiros-Borja C, Surpeta B, Thirunavukarasu AS, Dongmo Foumthuim CJ, Marchlewski I, Brezovsky J. J Chem Inf Model. 2024

2023

Preprint Rational engineering of binding pocket’s structure and dynamics in penicillin G acylase for selective degradation of bacterial signaling molecules. Grulich M, Surpeta B, Palyzová A, Marešová H, Zahradník J, Brezovsky J. bioRxiv. 2023 Preprint Impact of water models on structure and dynamics of ligand-transport tunnels in enzymes derived from molecular dynamics simulations. Agrawal N, Brezovsky J. bioRxiv. 2023 Publication Nano-structured hydrotrope-caged cytochrome c with boosted stability in harsh environments: a molecular insight. Bharadwaj P, Sarkar DK, Bisht M, Shet SM, Kotrappanavar NS, Lokesh V, Franklin G, Brezovsky J, Mondal D. Green Chem.. 2023 Publication Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters. Pakuła K, Sequeiros-Borja C, Biała-Leonhard W, Pawela A, Banasiak J, Bailly A, Radom M, Geisler M, Brezovsky J, Jasiński M. Cell Mol Life Sci.. 2023 Publication Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations. Sequeiros-Borja C, Surpeta B, Marchlewski I, Brezovsky J. MethodsX. 2023

2022

Publication Common Dynamic Determinants Govern Quorum Quenching Activity in N-Terminal Serine Hydrolases. Surpeta B, Grulich M, Palyzová A, Marešová H, Brezovsky J. ACS Catal. 2022 Publication TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them. Brezovsky J, Thirunavukarasu AS, Surpeta B, Sequeiros-Borja CE, Mandal N, Sarkar DK, Dongmo Foumthuim CJ, Agrawal N. Bioinformatics. 2022

2021

Recent advances in user-friendly computational tools to engineer protein function. Sequeiros-Borja CE, Surpeta B, Brezovsky J. Briefings in Bioinformatics. 2021

2020

Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering. Surpeta B, Sequeiros-Borja CE, Brezovsky J. Int J Mol Sci.. 2020

2018

CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Jurcik A, Bednar D, Byska J, Marques SM, Furmanova K, Daniel L, Kokkonen P, Brezovsky J, Strnad O, Stourac J, Pavelka A, Manak M, Damborsky J, Kozlikova B. Bioinformatics. 2018

2016

In-silico driven engineering of enantioselectivity of a penicillin G acylase towards active pharmaceutical ingredients. Grulich M, Brezovský J, Štěpánek V, Palyzová A, Marešová H, Zahradník J, Kyslíková E, Kyslík P. J Mol Catal B Enzym. 2016