| Recent advances in user-friendly computational tools to engineer protein function CE Sequeiros-Borja, B Surpeta, J Brezovsky Briefings in Bioinformatics 22 (3), bbaa150, 2021 | 65 | 2021 |
| Dynamics, a powerful component of current and future in silico approaches for protein design and engineering B Surpeta, CE Sequeiros-Borja, J Brezovsky International Journal of Molecular Sciences 21 (8), 2713, 2020 | 24 | 2020 |
| TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them J Brezovsky, AS Thirunavukarasu, B Surpeta, CE Sequeiros-Borja, ... Bioinformatics 38 (6), 1752-1753, 2022 | 14 | 2022 |
| Water will find its way: transport through narrow tunnels in hydrolases C Sequeiros-Borja, B Surpeta, AS Thirunavukarasu, ... Journal of Chemical Information and Modeling 64 (15), 6014-6025, 2024 | 6 | 2024 |
| Reinforcing tunnel network exploration in proteins using gaussian accelerated molecular dynamics N Mandal, B Surpeta, J Brezovsky Journal of Chemical Information and Modeling 64 (16), 6623-6635, 2024 | 4 | 2024 |
| Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites DK Sarkar, B Surpeta, J Brezovsky Journal of Chemical Theory and Computation 20 (14), 5807-5819, 2024 | 4 | 2024 |
| Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations C Sequeiros-Borja, B Surpeta, I Marchlewski, J Brezovsky MethodsX 10, 101968, 2023 | 4 | 2023 |
| Common dynamic determinants govern quorum quenching activity in N-terminal serine hydrolases B Surpeta, M Grulich, A Palyzová, H Marešová, J Brezovsky ACS Catalysis 12 (11), 6359-6374, 2022 | 4 | 2022 |
| Quorum Quenching Enzymes-Understanding Molecular Determinants Responsible for Activity of N-Terminal Serine Hydrolases to Increase their Strong Antibacterial Potency B Surpeta, M Grulich, J Brezovsky Biophysical Journal 120 (3), 305a, 2021 | 3 | 2021 |
| Computational tools for structural analysis of proteins J Brezovsky, A Sethi, B Surpeta Elsevier, 2024 | 1 | 2024 |
| Benchmarking coarse-grained simulation methods for investigation of transport tunnels in enzymes N Mandal, JA Stevens, AB Poma, B Surpeta, C Sequeiros-Borja, ... bioRxiv, 2024.09. 16.613244, 2024 | | 2024 |
| Rational engineering of binding pocket’s structure and dynamics in penicillin G acylase for selective degradation of bacterial signaling molecules M Grulich, B Surpeta, A Palyzová, H Marešová, J Zahradník, J Brezovsky bioRxiv, 2023.05. 09.538545, 2023 | | 2023 |
| Deciphering rare opening of gates in ligand-transport tunnels of enzymes using enhanced molecular dynamics simulations N Mandal, B Surpeta, J Brezovsky FEBS OPEN BIO 12, 249-249, 2022 | | 2022 |
| Engineering dynamic gates in binding pocket of penicillin G acylase to selectively degrade bacterial signaling molecules M Grulich, B Surpeta, A Palyzová, H Marešová, J Zahradník, J Brezovsky | | |
