Publications of Group Members
* - joint first authors; # - corresponding authors
Preprints
Mandal N, Stevens JA, Poma AB, Surpeta B, Sequeiros-Borja C, Thirunavukarasu AS, Marrink SJ, Brezovsky J, 2024: Benchmarking coarse-grained simulation methods for investigation of transport tunnels in enzymes. bioRxiv 2024.09.16.613244. full text
Grulich M,*# Surpeta B,* Palyzová A, Marešová H, Zahradník J, Brezovsky J,# 2023: Engineering dynamic gates in binding pocket of penicillin G acylase to selectively degrade bacterial signaling molecules. bioRxiv 2023.05.09.538545. full text dataset
2024
Thirunavukarasu AS, Szleper K, Tanriver G, Marchlewski I, Mitusinska K, Gora A,# Brezovsky J,# 2024: Water migration through enzyme tunnels is sensitive to choice of explicit water model. Journal of Chemical Information and Modeling: DOI:10.1021/acs.jcim.4c01177 full text dataset-DhaA dataset-CYP2D6+AldO
Sethi A,* Agrawal N,* Brezovsky J, 2024: Impact of water models on the structure and dynamics of enzyme tunnels. Computational and Structural Biotechnology Journal 23: 3946-3954. full text dataset
Mandal N, Surpeta B, Brezovsky J, 2024: Reinforcing Tunnel Network Exploration in Proteins using Gaussian Accelerated Molecular Dynamics. Journal of Chemical Information and Modeling 64: 6623-6635. full text dataset dataset-trajectories
Sarkar DK, Surpeta B, Brezovsky J, 2024: Incorporating prior knowledge in the seeds of adaptive sampling molecular dynamics simulations of ligand transport in enzymes with buried active sites. Journal of Chemical Theory and Computation 20: 5807-5819. full text dataset
Brezovsky J, Sethi A, Surpeta B, 2024: Computational Tools for Structural Analysis of Proteins. Reference Module in Life Sciences, Elsevier, DOI: 10.1016/B978-0-323-95502-7.00089-0 full text
Sequeiros-Borja C, Bartlomiej Surpeta, Thirunavukarasu AS, Dongmo Foumthuim CJ, Marchlewski I, Brezovsky J, 2024: Water will find its way: transport through narrow tunnels in hydrolases. Journal of Chemical Information and Modeling 64: 6014-6025. full text dataset-Hal dataset-Epx dataset-Lip dataset-hEpx dataset-E470G dataset-interactions dataset-Hal with different MD settings [front-cover]
Bharadwaj P, Shet SM, Bisht M, Sarkar DK, Franklin G, Nataraj SK, Mondal D, 2024: Suitability of adenosine derivatives in improving the activity and stability of cytochrome c under stress: Insights into the effect of phosphate groups. The Journal of Physical Chemistry B 128: 86-95. full text
2023
Bharadwaj P,* Sarkar DK,* Bisht M, Shet SM, Nataraj SK, Lokesh V, Franklin G,# Brezovsky J,# Mondal D,# 2023: Nano-structured hydrotrope-caged cytochrome c with boosted stability in harsh environments: a molecular insight. Green Chemistry 25: 6666-6676. full text dataset
Sequeiros-Borja C, Surpeta B, Marchlewski I, Brezovsky J, 2023: Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations. MethodsX 10C: 101968. full text dataset
Pakuła K,* Sequeiros-Borja C,* Biała-Leonhard W,* Pawela A, Banasiak J, Bailly A, Radom M, Geisler M, Brezovsky J,# Jasiński M,# 2023: Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters. Cellular and Molecular Life Sciences 80: 105. full text dataset
2022
Surpeta B, Grulich M, Palyzová A, Marešová H, Brezovsky J, 2022: Common Dynamic Determinants Govern Quorum Quenching Activity in N-Terminal Serine Hydrolases. ACS Catalysis 12: 6359-6374. full text dataset
Brezovsky J,# Thirunavukarasu AS, Surpeta B, Sequeiros-Borja CE, Mandal N, Sarkar DK, Dongmo Foumthuim CJ, Agrawal N, 2022: TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them. Bioinformatics 38: 1752-1753. full text dataset
2021
Sequeiros-Borja CE, Surpeta B, Brezovsky J, 2021: Recent advances in user-friendly computational tools to engineer protein function. Briefings in Bioinformatics 22: bbaa150. full text
2020
Surpeta B, Sequeiros-Borja CE, Brezovsky J, 2020: Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering. International Journal of Molecular Sciences 21: 2713. full text
Filipovic J, Vavra O, Plhak J, Bednar D, Marques SM, Brezovsky J, Matyska L, Damborsky J, 2020: CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE Transactions on Computational Biology and Bioinformatics 17: 1625-1638. full text
2019
Chrast L, Tratsiak K, Planas-Iglesias J, Daniel L, Prudnikova T, Brezovsky J, Bednar D, Kuta Smatanova I, Chaloupkova R, Damborsky J, 2019: Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17. Microorganisms 7: 498. full text
Vavra O, Filipovic J, Plhak J, Bednar D, Marques SM, Brezovsky J, Stourac J, Matyska L, Damborsky J, 2019: CaverDock: A Molecular Docking-Based Tool to Analyse Ligand Transport through Protein Tunnels and Channels. Bioinformatics 35: 4986-4993. full text
Stourac J, Vavra O, Kokkonen P, Filipovic J, Pinto G, Brezovsky J, Damborsky J, Bednar D, 2019: Caver Web 1.0: Identification of Tunnels and Channels in Proteins and Analysis of Ligand Transport. Nucleic Acids Research 46: W414-422. full text
2018
Kokkonen P, Sykora J, Prokop Z, Ghose A, Bednar D, Amaro M, Beerens K, Bidmanova S, Slanska M, Brezovsky J, Damborsky J, Hof M, 2018: Molecular Gating of an Engineered Enzyme Captured in Real Time. Journal of the American Chemical Society 140: 17999-18008. full text
Beerens K, Mazurenko S, Kunka A, Marques SM, Hansen N, Musil M, Chaloupkova R, Waterman J, Brezovsky J, Bednar D, Prokop Z, Damborsky J, 2018: Evolutionary Analysis is a Powerful Complement to Energy Calculations for Protein Stabilization. ACS Catalysis 8: 9420-9428. full text
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, 2018: CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics 34: 3586-3588. full text
Kaushik S, Marques SM, Khirsariya P, Paruch K, Libichova L, Brezovsky J, Prokop Z, Chaloupkova R, Damborsky J, 2018: Impact of the Access Tunnel Engineering on Catalysis is Strictly Ligand-Specific. FEBS Journal 285: 1456-1476. full text
Vanacek P, Sebestova E, Babkova P, Bidmanova S, Daniel L, Dvorak P, Stepankova V, Chaloupkova R, Brezovsky J, Prokop Z, Damborsky J, 2018: Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catalysis 8: 2402-2412. full text
Brezovsky J, Kozlikova B, Damborsky J, 2018: Computational Analysis of Protein Tunnels and Channels. In: Bornscheuer U., Höhne M. (eds) Protein Engineering. Methods in Molecular Biology, vol 1685. Humana Press, New York, NY, pp. 25-42. full text
Dvorak P, Bednar D, Vanacek P, Balek L, Eiselleova L, Stepankova V, Sebestova E, Kunova Bosakova M, Konecna Z, Mazurenko S, Kunka A, Vanova T, Zoufalova K, Chaloupkova R, Brezovsky J, Krejci P, Prokop Z, Dvorak P, Damborsky J, 2018: Computer-Assisted Engineering of Hyperstable Fibroblast Growth Factor 2. Biotechnology and Bioengineering 115: 850-862. full text
2017
Marques SM, Daniel L, Buryska T, Prokop Z, Brezovsky J, Damborsky J, 2017: Enzyme Tunnels and Gates as Relevant Targets in Drug Design. Medicinal Research Reviews 37: 1095-1139. full text
Marques SM, Dunajova Z, Prokop Z, Chaloupkova R, Brezovsky J, Damborsky J, 2017: Catalytic Cycle of Haloalkane Dehalogenases towards Unnatural Substrates Explored by Computational Modeling. Journal of Chemical Information and Modeling 57: 1970–1989. full text
Musil M, Stourac J, Bendl J, Brezovsky J, Prokop Z, Zendulka J, Martinek T, Bednar D, Damborsky J, 2017: FireProt: Web Server for Automated Design of Thermostable Proteins. Nucleic Acids Research 45: W393-399. full text
Babkova P, Sebestova E, Brezovsky J, Chaloupkova R, Damborsky J, 2017: Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity. ChemBioChem 18: 1448-1456. full text
Liskova V, Stepankova V, Bednar D, Brezovsky J, Prokop Z, Chaloupkova R, Damborsky J, 2017: Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear β-Haloalkanes: Open–Solvated versus Occluded–Desolvated Active Sites. Angewandte Chemie International Edition 56: 4719–4723. full text
2016
Grulich M, Brezovsky J, Stepanek V, Palyzova A, Maresova H, Zahradnik J, Kyslikova E, Kyslik P, 2016: In-silico Driven Engineering of Enantioselectivity of a Penicillin G Acylase towards Active Pharmaceutical Ingredients. Journal of Molecular Catalysis B: Enzymatic 133: S53-S59. full text.
Brezovsky J,* Babkova P,* Degtjarik O, Fortova A, Gora A, Iermak I, Rezacova P, Dvorak P, Kuta Smatanova I, Prokop Z, Chaloupkova R, Damborsky J, 2016: Engineering a De Novo Transport Tunnel. ACS Catalysis 6: 7597-7610. full text
Bendl J, Musil M, Stourac J, Zendulka J, Damborsky J,# Brezovsky J,# 2016: PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. PLoS Computational Biology 12: e1004962. full text
Bendl J, Stourac J, Sebestova E, Vavra O, Musil M, Brezovsky J,# Damborsky J,# 2016: HotSpot Wizard 2: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering. Nucleic Acids Research 44: W479-487. full text
Pavelka A, Kozlíkova B, Sochor J, Sebestova E, Brezovsky J, Damborsky J, 2016: CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. IEEE Transactions on Computational Biology and Bioinformatics 13: 505-517. full text
Ison J, Rapacki K, Menager H, Kalas M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, et al., 2016: Tools and Data Services Registry: a Community Effort to Document Bioinformatics Resources. Nucleic Acids Research 44: D38-47. full text
Buryska T, Daniel L, Kunka A, Brezovsky J, Damborsky J, Prokop Z, 2016: Discovery of Novel Haloalkane Dehalogenase Inhibitors. Applied and Environmental Microbiology 82: 1958-1965. full text
Marques SM, Brezovsky J, Damborsky J, 2016: Role of Tunnels and Gates in Enzymatic Catalysis. In: Svendsen A, Understanding Enzymes: Function, Design, Engineering, and Analysis, Pan Stanford Publishing, pp. 421-463. full text
2015
Daniel L, Buryska T, Prokop Z, Damborsky J, Brezovsky J, 2015: Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases using in Silico Screening. Journal of Chemical Information and Modeling 55: 54-62. full text
Amaro M, Brezovsky J, Kovacova S, Sykora J, Bednar D, Nemec V, Liskova V, Kurumbang NP, Beerens K, Chaloupkova R, Paruch K, Hof M, Damborsky J, 2015: Site-Specific Analysis of Protein Hydration Based on Unnatural Amino Acid Fluorescence. Journal of the American Chemical Society 137: 4988-4992. full text
Grulich M, Brezovsky J, Stepanek V, Palyzova A, Kyslikova E, Kyslik P, 2015: Resolution of α/β-Amino Acids by Enantioselective Penicillin G Acylase from Achromobacter sp. Journal of Molecular Catalysis B: Enzymatic 122: 240-247. full text
Liskova V, Bednar D, Holubeva T, Prudnikova T, Rezacova P, Koudelakova T, Sebestova E, Kuta Smatanova I, Brezovsky J, Chaloupkova R, Damborsky J, 2015: Balancing the Stability-Activity Trade-off by Fine-Tuning Dehalogenase Access Tunnels. ChemCatChem 7: 648-659. full text
Bednar D, Beerens K, Sebestova E, Bendl J, Khare S, Chaloupkova R, Prokop Z, Brezovsky J, Baker D, Damborsky J, 2015: FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLoS Computational Biology 11: e1004556. full text
Nehybova T, Smarda J, Daniel L, Brezovsky J, Benes P, 2015: Wedelolactone Induces Growth of Breast Cancer Cells by Stimulation of Estrogen Receptor Signalling. Journal of Steroid Biochemistry and Molecular Biology 152: 76-83. full text
2014
Sykora J,* Brezovsky J,* Koudelakova T,* Lahoda M, Fortova A, Chernovets T, Chaloupkova R, Stepankova V, Prokop Z, Kuta Smatanova I, Hof M, Damborsky J, 2014: Dynamics and Hydration Explain Failed Functional Transformation in Dehalogenase Design. Nature Chemical Biology 10: 428-430. full text
Damborsky J, Brezovsky J, 2014: Computational Tools for Designing and Engineering Enzymes. Current Opinion in Chemical Biology 19: 8-16. full text
Bendl J, Stourac J, Salanda O, Pavelka A, Wieben ED, Zendulka J, Brezovsky J,# Damborsky J,# 2014: PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations. PLoS Computational Biology 10: e1003440. full text
Kozlikova B, Sebestova E, Sustr V, Brezovsky J, Strnad O, Daniel L, Bednar D, Pavelka A, Manak M, Bezdeka M, Benes P, Kotry M, Gora A, Damborsky J, Sochor J, 2014: CAVER Analyst 1.0: Graphic Tool for Interactive Visualization and Analysis of Tunnels and Channels in Protein Structures. Bioinformatics 30: 2684-2685. full text
Kurumbang NP, Dvorak P, Bendl J, Brezovsky J, Prokop Z, Damborsky J, 2014: Computer-Assisted Engineering of Synthetic Pathway for Biodegradation of Toxic Persistent Pollutant. ACS Synthetic Biology 3: 172–181. full text
Dvorak P, Kurumbang NP, Bendl J, Brezovsky J, Prokop Z, Damborsky J, 2014: Maximizing the Efficiency of Multi-enzyme Process by Stoichiometry Optimization. ChemBioChem 15: 1891-1895. full text
Chavarria M, Durante-Rodriguez G, Krell T, Santiago C, Brezovsky J, Damborsky J, de Lorenzo V, 2014: Fructose 1-Phosphate is the One and Only Physiological Effector of the Cra (FruR) Regulator of Pseudomonas putida. FEBS Open Bio 4: 377-386. full text
Chaloupkova R, Prudnikova T, Rezacova P, Prokop Z, Koudelakova T, Daniel L, Brezovsky J, Ikeda-Ohtsubo W, Sato Y, Kuty M, Nagata Y, Kuta Smatanova I, Damborsky J, 2014: Structural and Functional Analysis of a Novel Haloalkane Dehalogenase with Two Halide-Binding Sites. Acta Crystallographica D 70: 1884-1897. full text
2013
Gora A, Brezovsky J, Damborsky J, 2013: Gates of Enzymes. Chemical Reviews 113: 5871–5923. full text
Brezovsky J, Chovancova E, Gora A, Pavelka A, Biedermannova L, Damborsky J, 2013: Software Tools for Identification, Visualization and Analysis of Protein Tunnels and Channels. Biotechnology Advances 31: 38-49. full text
Koudelakova T, Chaloupkova R, Brezovsky J, Prokop Z, Sebestova E, Hesseler M, Khabiri M, Plevaka M, Kulik D, Kuta Smatanova I, Rezacova P, Ettrich R, Bornscheuer UT, Damborsky J, 2013: Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel. Angewandte Chemie International Edition 52: 1959-1963. full text
Amaro M, Brezovsky J, Kovacova S, Maier L, Chaloupkova R, Sykora J, Paruch K, Damborsky J, Hof M, 2013: Are Time-Dependent Stokes Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore? Journal of Physical Chemistry B 117: 7898-7906. full text
Stepankova V, Khabiri M, Brezovsky J, Pavelka A, Sykora J, Amaro M, Minofar B, Prokop Z, Hof M, Ettrich R, Chaloupkova R, Damborsky J, 2013: Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents. ChemBioChem 14: 890-897. full text
Hasan K, Gora A, Brezovsky J, Chaloupkova R, Moskalikova H, Fortova A, Nagata Y, Damborsky J, Prokop Z, 2013: The Effect of a Unique Halide-Stabilising Residue on the Catalytic Properties of Haloalkane Dehalogenase DatA from Agrobacterium tumefaciens C58. FEBS Journal 280: 3149-3159. full text
Khabiri M, Minofar B, Brezovsky J, Damborsky J, Ettrich R, 2013: Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface. Journal of Molecular Modeling 19: 4701-4711. full text
2012
Chovancova E, Pavelka A, Benes P, Strnad O, Brezovsky J, Kozlikova B, Gora A, Sustr V, Klvana M, Medek P, Biedermannova L, Sochor J, Damborsky J, 2012: CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Computational Biology 8: e1002708. full text
Prokop Z, Gora A, Brezovsky J, Chaloupkova R, Stepankova V, Damborsky J, 2012: Engineering of Protein Tunnels: Keyhole-lock-key Model for Catalysis by the Enzymes with Buried Active Sites. In: Lutz, S., Bornscheuer, U.T. (Eds.), Protein Engineering Handbook, Wiley-VCH, Weinheim, pp. 421-464. full text
2011
Kobeticova K, Simek Z, Brezovsky J, Hofman J, 2011: Toxic Effects of Nine Polycyclic Aromatic Compounds on Enchytraeus crypticus in Artificial Soil in Relation to their Properties. Ecotoxicology and Environmental Safety 74: 1727-1733. full text
Koudelakova T, Chovancova E, Brezovsky J, Monincova M, Fortova A, Jarkovsky J, Damborsky J, 2011: Substrate Specificity of Haloalkane Dehalogenases. Biochemical Journal 435: 345-354. full text
2010
Prokop Z,* Sato Y,* Brezovsky J,* Mozga T, Chaloupkova R, Koudelakova T, Jerabek P, Stepankova V, Natsume R, Leeuwen JGE, Janssen DB, Florian J, Nagata Y, Senda T, Damborsky J, 2010: Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering. Angewandte Chemie International Edition 49: 6111-6115. full text
2009
Damborsky J, Brezovsky J, 2009: Computational Tools for Designing and Engineering Biocatalysts. Current Opinion in Chemical Biology 13: 26-34. full text
Jesenska A, Sykora J, Olzynska A, Brezovsky J, Zdrahal Z, Damborsky J, Hof M, 2009: Nanosecond Time-Dependent Stokes Shift at the Tunnel Mouth of Haloalkane Dehalogenases. Journal of the American Chemical Society 131: 494-501. full text