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

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

Impact of water models on the structure and dynamics of enzyme tunnels.

Sethi A, Agrawal N, Brezovsky J.

Comput Struct Biotechnol J. 2024

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

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

Mandal N, Surpeta B, Brezovsky J.

J Chem Inf Model. 2024

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

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

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

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

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

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

Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations.

Sequeiros-Borja C, Surpeta B, Marchlewski I, Brezovsky J.

MethodsX. 2023

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

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

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

Sequeiros-Borja CE, Surpeta B, Brezovsky J.

Briefings in Bioinformatics. 2021

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

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

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