Publications of Group Members

* - joint first authors; # - corresponding authors


Mandal N, Surpeta B, Brezovsky J, 2024: Reinforcing Tunnel Network Exploration in Proteins using Gaussian Accelerated Molecular Dynamics. bioRxiv 2024.04.30.591887. full text dataset dataset-trajectories

Thirunavukarasu AS, Szleper K, Tanriver G, Mitusinska K, Gora A,# Brezovsky J,# 2023: Water migration through enzyme tunnels is sensitive to choice of explicit water model. bioRxiv . full text dataset-DhaA

Grulich M,*# Surpeta B,* Palyzová A, Marešová H, Zahradník J, Brezovsky J,# 2023: Rational engineering of binding pocket’s structure and dynamics in penicillin G acylase for selective degradation of bacterial signaling molecules. bioRxiv 2023.05.09.538545. full text dataset

Agrawal N, Brezovsky J, 2023: Impact of water models on structure and dynamics of ligand-transport tunnels in enzymes derived from molecular dynamics simulations. bioRxiv 2023.04.19.537534. full text dataset


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

Sequeiros-Borja C, Bartlomiej Surpeta, Thirunavukarasu AS, Dongmo Foumthuim CJ, Igor Marchlewski, Brezovsky J, 2024: Water will find its way: transport through narrow tunnels in hydrolases. Journal of Chemical Information and Modeling, DOI: 10.1021/acs.jcim.4c00094. full text dataset-Hal dataset-Epx dataset-Lip dataset-hEpx dataset-E470G dataset-interactions dataset-Hal with different MD settings

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


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 Chemistry25: 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


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


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


Surpeta B, Sequeiros-Borja CE, Brezovsky J, 2020: Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and EngineeringInternational 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 TransportIEEE Transactions on Computational Biology and Bioinformatics 17: 1625-1638. full text


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


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

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


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


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


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


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


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


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


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


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


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