Publications
2024
Velecky, J., Berezny, M., Musil, M., Damborsky, J., Bednar, D., Mazurenko, S., 2024: BenchStab: a Tool for Automated Querying of Web-Based Stability Predictors. Bioinformatics XX: xxx-xxx.
Mican, J., Jaradat, D. M. M., Liu, W., Weber, G., Mazurenko, S., Bornscheuer, U. T., Damborsky, J., Wei, R., Bednar, D., 2024: Exploring New Galaxies: Perspectives on the Discovery of Novel PET-Degrading Enzymes. Applied Catalysis B: Environment and Energy 342: 1-16.
Musil, M., Jezik, A., Horackova, J., Borko, S., Kabourek, P., Damborsky, J., Bednar, D., 2024: FireProt 2.0: Web-based Platform for the Fully Automated Design of Thermostable Proteins. Briefings in Bioinformatics 25: 1-10.
Schäfer, M., Brich, N., Byska, J., Marques, S. M., Bednar, D., Thiel, P., Kozlikova, B., Krone, M., 2024: InVADo: Interactive Visual Analysis of Molecular Docking Data. IEEE Transactions on Visualization and Computer Graphics 30: 1984-1997.
Fruhauf, S., Pühringer, D., Thamhesl, M., Fajtl, P., Kunz-Vekiru, E., Höbartner-Gussl, A., Schatzmayr, G., Adam, G., Damborsky, J., Djinovic-Carugo, K., Prokop, Z., Moll, W.-D., 2024: Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone. ACS Catalysis 14: 3392–3410.
de La Bourdonnaye, G., Ghazalova, T., Fojtik, P., Kutalkova, K., Bednar, D., Damborsky, J., Rotrekl, V., Stepankova, V., Chaloupkova, R., 2024: Computer-Aided Engineering of Stabilized Fibroblast Growth Factor 21. Computational and Structural Biotechnology Journal 23: 942-951.
Martin, H. G., Mazurenko, S., Zhao, H., 2024: Special Issue on Artificial Intelligence for Synthetic Biology. ACS Synthetic Biology 13: 408–410.
Planas-Iglesias, J., Borko, S., Swiatkowski, J., Elias, M., Havlasek, M., Salamon, O., Grakova, E., Kunka, A., Martinovic, T., Damborsky, J., Martinovic, J., Bednar, D., 2024: AggreProt: A Web Server for Predicting and Engineering Aggregation Prone Regions in Proteins. Nucleic Acids Research gkae420: 1-11.
Marques, S. M., Kouba, P., Legrand, A., Sedlar, J., Disson, L., Planas-Iglesias, J., Sanusi, Z., Kunka, A., Damborsky, J., Pajdla, T., Prokop, Z., Mazurenko, S., Sivic, J., Bednar, D., 2024: CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS Au 4: 2228-2245.
Harding-Larsen, D., Degnbol Madsen, C., Teze, D., Kittilä, T., Rosander Langhorn, M., Gharabli, H., Hobusch, M., Mejia Otalvaro, F., Kırtel, O., Nahuel Bidart, G., Mazurenko, S., Travnik, E., Hededam Welner, D., 2024: GASP: A Pan-Specific Predictor of Family 1 Glycosyltransferase Acceptor Specificity Enabled by a Pipeline for Substrate Feature Generation and Large-Scale Experimental Screening. ACS Omega 4: 2228-2245.
Slanska, M., Stackova, L., Marques, S. M., Stacko, P., Martinek, M., Jilek, L., Toul, M., Damborsky, J., Bednar, D., Klan, P., Prokop, Z., 2024: Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family. ACS Catalysis 14: 11635-11645.
Opaleny, F., Ulbrich, P., Planas-Iglesias, J., Byska, J., Stourac, J., Bednar, D., Furmanova, K., Kozlikova, B., 2024: Visual Support for the Loop Grafting Workflow on Proteins. IEEE Transactions on Visualization and Computer Graphics (TVCG) 1: 1-11.
Kandra, M., Vanova, T., Jongen, V. A., Pospisil, J., Novak, J., Chochola, V., Buryska, T., Prokop, Z., Hodny, Z., Hampl, A., Bohaciakova, D., Jaros, J. , 2024: A Closed 3D Printed Microfluidic Device for Automated Growth and Differentiation of Cerebral Organoids from Single-Cell Suspension. Biotechnology Journal 19: 1-17.
2023
Holoubek, J., Lipovy, B., Knoz, M., Kempny, T., Chaloupkova, R., Damborsky, J., Vojtova, L., 2023: The Future for the Application of Fibroblast Growth Factor 2 in Modern Wound Healing. Burns 49: 484-486.
Schenkmayerova, A., Toul, M., Pluskal, D., Baatallah, R., Gagnot, G., Pinto, G. P., Santana, V. T., Stuchla, M., Neugebauer, P., Chaiyen, P., Damborsky, J., Bednar, D., Janin, Y. L., Prokop, Z., Marek, M., 2023: Catalytic Mechanism for Renilla-type Luciferases. Nature Catalysis 6: 23-38.
Carna, M., Onyango, I. G., Katina, S., Holub, D., et al., 2023: Pathogenesis of Alzheimer’s Disease: Involvement of the Choroid Plexus. Alzheimer's & Dementia: 1-18.
Vasina, M., Kovar, D., Damborsky, J., Ding, Y., Yang, T., deMello, A., Mazurenko, S., Stavrakis, S., Prokop, Z., 2023: In-depth Analysis of Biocatalysts by Microfluidics: An Emerging Source of Data for Machine Learning. Biotechnology Advances 66: 108171.
Kouba, P., Kohout, P., Haddadi, F., Bushuiev, A., Samusevich, R., Sedlar, J., Damborsky, J., Pluskal, T., Sivic, J., Mazurenko, S., 2023: Machine Learning-Guided Protein Engineering. ACS Catalysis 13: 13863-13895.
Toul, M., Slonkova, V., Mican, J., Urminsky, A., Tomkova, M., Sedlak, E., Bednar, D., Damborsky, J., Hernychova, L., Prokop, Z., 2023: Identification, Characterization, and Engineering of Glycosylation in Thrombolytics. Biotechnology Advances 66: 108174.
Nemergut, M., Marques, S. M., Uhrik, L., Vanova, T., Nezvedova, M., Gadara, D. C., Jha, D., Tulis, J., Novakova, V., Planas-Iglesias, J., Kunka, A., Legrand, A., Hribkova, H., Pospisilova, V., Sedmik, J., Raska, J., Prokop, Z., Damborsky, J., Bohaciakova, D., Spacil, Z., Hernychova, L., Bednar, D., Marek, M., 2023: Domino-like Effect of C112R Mutation on ApoE4 Aggregation and Its Reduction by Alzheimer’s Disease Drug Candidate. Molecular Neurodegeneration 18: 38.
Poljovka, A, Musil, M., Bednar, D., Chovanova, K., Bauerova-Hlinkova, V., Bellova, J., Kohutova, L., Barath, P., Zamocky, M., 2023: Comparison of Fungal Thermophilic and Mesophilic Catalase-Peroxidases for Their Antioxidative Properties. Antioxidants 12: 1382.
Vavra, O., Beranek, J., Stourac, J., Surkovsky, M., Filipovic, J., Damborsky, J., Martinovic, J., Bednar, D., 2023: pyCaverDock: Python Implementation of the Popular Tool for Analysis of Ligand Transport with Advanced Caching and Batch Calculation Support. Bioinformatics 39: btad443.
Chmelova, K., Gao, T., Polak, M., Schenkmayerova, A., Croll, T. I., Shaikh, T. R., Skarupova, J., Chaloupkova, R., Diederichs, K., Read, R. J., Damborsky, J., Novacek, J., Marek, M. , 2023: Multimeric Structure of a Subfamily III Haloalkane Dehalogenase-like Enzyme Solved by Combination of Cryo-EM and X-ray Crystallography. Protein Science 32: e4751.
Kunka, A., Marques, S. M., Havlasek, M., Vasina, M., Velatova, N., Cengelova, L., Kovar, D., Damborsky, J., Marek, M., Bednar, D., Prokop, Z., 2023: Advancing Enzyme’s Stability and Catalytic Efficiency through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning. ACS Catalysis 13: 12506–12518.
Nemergut, M., Pluskal, D., Horackova, J., Sustrova, T., Tulis, J., Barta, T., Baatallah, R., Gagnot, G., Novakova, V., Majerova, M., Sedlackova, K., Marques, S. M., Toul, M., Damborsky, J., Prokop, Z., Bednar, D., Janin, Y. L., Marek, M., 2023: Illuminating the Mechanism and Allosteric Behavior of NanoLuc Luciferase. Nature Communications 14: 7864.
Spackova, A., Vavra, O., Racek, T., Bazgier, V., Sehnal, D., Damborsky, J., Svobodova, R., Bednar, D., Berka, K., 2023: ChannelsDB 2.0: a Comprehensive Database of Protein Tunnels and Pores in AlphaFold Era. Nucleic Acids Research: gkad1012: 1-6.
Papageorgiou, A. C., Pospisilova, M., Cibulka, J., Ashraf, R., Waudby, C. A., Kadeřávek, P., Maroz, V., Kubicek, K., Prokop, Z., Krejci, L., Tripsianes, K., 2023: Recognition and Coacervation of G-Quadruplexes by a Multifunctional Disordered Region in RECQ4 Helicase. Nature Communications 14: 6751.
Fulneček, J., Klimentová, E., Cairo, A., Bukovcakova, S. V., Alexiou, P., Prokop, Z., Riha, K., 2023: The SAP Domain of Ku Facilitates its Efficient Loading onto DNA Ends. Nucleic Acids Research gkad850: 1-11.
Snajdarova, K., Marques, S. M., Damborsky, J., Bednar, D., Marek, M., 2023: Atypical Homodimerization Revealed by the Structure of the (S)-Enantioselective Haloalkane Dehalogenase DmmarA from Mycobacterium marinum. Acta Crystallographica Section D Structural Biology 79: 956-970.
Vilim, J., Ghazalova, T., Petulova, E., Horackova, A., Stepankova, V., Chaloupkova, R., Bednar, D., Damborsky, J., Prokop, Z., 2023: Computer-Assisted Stabilization of Fibroblast Growth Factor FGF-18. Computational and Structural Biotechnology Journal 21: 5144-5152.
Gao, T., Damborsky, J., Janin, Y. L., Marek, M., 2023: Deciphering Enzyme Mechanisms with Engineered Ancestors and Substrate Analogues. ChemCatChem 15: e202300745.
2022
Pfaff, L., Gao, J., Li, Z., Jäckering, A., Weber, G., Mican, J., Chen, Y., Dong, W., Han, X., Feiler, C. G., Ao, Y.-F., Badenhorst, C. P. S., Bednar, D., Palm, G. J., Lammers, M., Damborsky, J., Strodel, B., Liu, W., Bornscheuer, U. T., Wei, R., 2022: Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase. ACS Catalysis 12: 9790-9800.
von Haugwitz, G., Han, X., Pfaff, L., Li, Q., Wei, H., Gao, J., Methling, K., Ao, Y., Brack, Y., Mican, J., Feiler, C. G., Weiss, M. S., Bednar, D., Palm, G. J., Lalk, M., Lammers, M., Damborsky, J., Weber, G., Liu, W., Bornscheuer, U. T., Wei, R., 2022: Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization. ACS Catalysis 12: 15259–15270.
Musil, M., Jezik, A., Jankujova, M., Stourac, J., Galgonek, J., Eyrilmez, S. M., Vondrasek, J., Damborsky, J., Bednar, D., 2022: Fully Automated Virtual Screening Pipeline of FDA-Approved Drugs Using Caver Web. Computational and Structural Biotechnology Journal 20: 6512-6518.
Yang, T., Villois, A., Kunka, A., Grigolato, F., Arosio, P., Prokop, Z., deMello, A., Stavrakis, S., 2022: Droplet-Based Microfluidic Temperature-Jump Platform for the Rapid Assessment of Biomolecular Kinetics. Analytical Chemistry 94: 16675–16684.
Velecky, J., Hamsikova, M., Stourac, J., Musil, M., Damborsky, J., Bednar, D., Mazurenko, S., 2022: SoluProtMutDB: A Manually Curated Database of Protein Solubility Changes Upon Mutations. Computational and Structural Biotechnology Journal 20: 6339-6347.
Bouchalova, P., Sommerova, L., Potesil, D., Martisova, A., Lapcik, P., Koci, V., Scherl, A., Vonka, P., Planas-Iglesias, J., Chevet, E., Bouchal, P., Hrstka, R., 2022: Characterization of the AGR2 Interactome Uncovers New Players of Protein Disulfide Isomerase Network in Cancer Cells. Molecular & Cellular Proteomics 21: 100188.
Pospisil, J., Hrabovsky, M., Bohaciakova, D., Hovadkova, Z., Jurasek, M., Mlcouskova, J., Paruch, K., Nevolova, S., Damborsky, J., Hampl, A., Jaros, J. , 2022: Geometric Control of Cell Behavior by Biomolecule Nanodistribution. ACS Biomaterials Science & Engineering 8: 4789-4806.
Vasina, M., Vanacek, P., Hon, J., Kovar, D., Faldynova, H., Kunka, A., Buryska, T., Badenhorst, C.P.S., Mazurenko, S., Bednar, D., Stavrakis, S., Bornscheuer, U.T., deMello, A., Damborsky, J., Prokop, Z., 2022: Advanced Database Mining of Efficient Biocatalysts by Sequence and Structure Bioinformatics and Microfluidics. Chem Catalysis 2: 2704-2725.
Ulbrich, P., Waldner, M., Furmanova, K., Marques, S.M., Bednar, D., Kozlikova, B., Byska, J., 2022: sMolBoxes: Dataflow Model for Molecular Dynamics Exploration. IEEE Transactions on Visualization and Computer Graphics 29: 581-590.
Toul, M., Mican, J., Slonkova, V., Nikitin, D., Marek, M., Bednar, D., Damborsky, J., Prokop, Z., 2022: Hidden Potential of Highly Efficient and Widely Accessible Thrombolytic Staphylokinase. Stroke 53: 3235-3237.
Horak, M., Fairweather, D., Kokkonen, P., Bednar, D., Bienertova-Vasku, J., 2022: Follistatin‑like 1 and Its Paralogs in Heart Development and Cardiovascular Disease. Heart Failure Reviews: 2022.
Pinto, G. P., Hendrikse, N. M., Stourac, J., Damborsky, J., Bednar, D., 2022: Virtual Screening of Potential Anticancer Drugs Based on Microbial Products. Seminars in Cancer Biology 86: 1207-1217.
Wei, R., von Haugwitz, G., Pfaff, L., Mican, J., Badenhorst, C. P. S., Liu, W., Weber, G., Austin, H. P., Bednar, D., Damborsky, J., Bornscheuer, U. T., 2022: Mechanistic-based Design of Efficient PET Hydrolases. ACS Catalysis 12: 3382-3396.
Rapp, L. R., Marques, S. M., Nebel, B., Damborsky, J., Hauer, B., 2022: Engineering CYP153AM.aq to Oxyfunctionalize its Inhibitor Dodecylamine Using a LC/MS Based Rapid Flow Analysis Screening. ChemCatChem: e202101648.
Vasina, M., Velecky, J., Planas-Iglesias, J., Marques, S. M., Skarupova, J., Damborsky, J., Bednar, D., Mazurenko, S., Prokop, Z., 2022: Tools for Computational Design and High-Throughput Screening of Therapeutic Enzymes. Advanced Drug Delivery Reviews 183: 114143.
Toul, M., Nikitin, D., Marek, M., Damborsky, J., Prokop, Z., 2022: Extended Mechanism of the Plasminogen Activator Staphylokinase Revealed by Global Kinetic Analysis: 1000-fold Higher Catalytic Activity than That of Clinically Used Alteplase. ACS Catalysis 12: 3807-3814.
Nikitin, D., Mican, J., Toul, M., Bednar, D., Peskova, M., Kittova, P., Thalerova, S., Vitecek, J., Damborsky, J., Mikulik, R., Fleishman, S. J., Prokop, Z., Marek, M., 2022: Computer-Aided Engineering of Staphylokinase Toward Enhanced Affinity and Selectivity for Plasmin. Computational and Structural Biotechnology Journal 20: 1366-1377.
Zamocky, M., Musil, M., Danchenko, M., Ferianc, P., Chovanova, K., Barath, P., Poljovka, A., Bednar, D., 2022: Deep Insights into the Specific Evolution of Fungal Hybrid B Heme Peroxidases. Biology 11: 459.
Pardo, I., Bednar, D., Calero, P., Volke, D. C., Damborsky, J., Nikel, P. I., 2022: A Non-conventional Archaeal Fluorinase Identified by in silico Mining for Enhanced Fluorine Biocatalysis. ACS Catalysis 12: 6570–6577.
Kunka, A., Lacko, D., Stourac, J., Damborsky, J., Prokop, Z., Mazurenko, S., 2022: CalFitter 2.0: Leveraging the Power of Singular Value Decomposition to Analyse Protein Thermostability. Nucleic Acids Research gkac378: 1-7.
Marques, S. M., Slanska, M., Chmelova, K., Chaloupkova, R., Marek, M., Clark, S., Damborsky, J., Kool, E. T., Bednar, D., Prokop, Z., 2022: Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling. JACS Au 2: 1324−1337.
Prakinee, K., Phintha, A., Visitsatthawong, S., Lawan, N., Sucharitakul, J., Kantiwiriyawanitch, C., Damborsky, J., Chitnumsub, P., van Pée, K.-H., Chaiyen, P., 2022: Mechanism-Guided Tunnel Engineering to Increase the Efficiency of a Flavin-Dependent Halogenase. Nature Catalysis 5: 534-544.
Vavra, O., Damborsky, J., Bednar, D., 2022: Fast Approximative Methods for Study of Ligand Transport and Rational Design of Improved Enzymes for Biotechnologies. Biotechnology Advances 60: 108009.
Nemergut, M., Batkova, T., Vigasova, D., Bartos, M., Hlozankova, M., Schenkmayerova, A., Liskova, B., Sheardova, K., Vyhnalek, M., Hort, J., Laczo, J., Kovacova, I., Sitina, M., Matej, R., Jancalek, R., Marek, M., Damborsky, J., 2022: Increased Occurrence of Treponema spp. and Double-Species Infections in Patients with Alzheimer’s Disease. Science of The Total Environment 844: 1-7.
Planas-Iglesias, J., Opaleny, F., Ulbrich, P., Stourac, J., Sanusi, Z., Pinto, G. P., Schenkmayerova, A., Byska, J., Damborsky, J., Kozlikova, B., Bednar, D., 2022: LoopGrafter: a Web Tool for Transplanting Dynamical Loops for Protein Engineering. Nucleic Acids Research 50 (W1): W465–W473.
2021
Marques, S. M., Planas-Iglesias, J., Damborsky, J., 2021: Web-based Tools for Computational Enzyme Design. Current Opinion in Structural Biology 69: 19-34.
Gorecki, L., Misiachna, A., Damborsky, J., Dolezal, R., Korabecny, J., Cejkova, L., Hakenova, K., Chvojkova, M., Zdarova Karasova, J., Prchal, L., Novak, M., Kolcheva, M., Kortus, S., Vales, S., Horak, M., Soukup, O., 2021: Structure-Activity Relationships of Dually-Acting Acetylcholinesterase Inhibitors Derived from Tacrine on N-Methyl-D-Aspartate Receptors. European Journal of Medicinal Chemistry 219: 113434.
Khan, R. T., Musil, M., Stourac, J., Damborsky, J., Bednar, D., 2021: Fully Automated Ancestral Sequence Reconstruction using FireProtASR. Current Protocols 1: e30.
Mazur, A., Prudnikova, T., Grinkevich, P., Mesters, J. R., Mrazova, D., Chaloupkova, R., Damborsky, J., Kuty, M., Kolenko, P., Kuta Smatanova, I., 2021: The Tetrameric Structure of a Novel Haloalkane Dehalogenase DpaA from Paraglaciecola agarilytica NO2. Acta Crystallographica Section D77: 347-356.
Planas-Iglesias, J., Marques, S. M., Pinto, G. P., Musil, M., Stourac, J., Damborsky, J., Bednar, D., 2021: Computational Design of Enzymes for Biotechnological Applications. Biotechnology Advances 47: 107696.
Vigasova, D., Nemergut, M., Liskova, B., Damborsky, J., 2021: Multi-pathogen Infections and Alzheimer’s Disease. Microbial Cell Factories 20: 1-13.
Hon, J., Marusiak, M., Martinek, T., Kunka, A., Zendulka, J., Bednar, D., Damborsky, J., 2021: SoluProt: Prediction of Soluble Protein Expression in Escherichia coli. Bioinformatics 37: 23-28.
Iermak, I., Degtjarik, O., Havlickova, P., Kuty, M., Chaloupkova, R., Damborsky, J., Prudnikova, T., Kuta Smatanova, I., 2021: Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum. Catalysts 11: 5.
Kokkonen, P., Beier, A., Mazurenko, S., Damborsky, J., Bednar, D., Prokop, Z., 2021: Substrate Inhibition by the Blockage of Product Release and Its Control by Tunnel Engineering. RSC Chemical Biology 2: 645-655.
Nikitin, D., Choi, S., Mican, J., Toul, M., Ryu, W.-S., Damborsky, J., Mikulik, R., Kim, D.-E., 2021: Development and Testing of Thrombolytics in Stroke. Journal of Stroke 23: 12-36.
Musil, M., Khan, R. T., Beier, A., Stourac, J., Konegger, H., Damborsky, J., Bednar, D., 2021: FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction. Briefings in Bioinformatics 22: 1-11.
Rapp, L. R., Marques, S. M., Zukic, E., Rowlinson, B., Sharma, M., Grogan, G., Damborsky, J., Hauer, B., 2021: Substrate Anchoring and Flexibility Reduction in CYP153AM.aq Leads to Highly Improved Efficiency towards Octanoic Acid. ACS Catalysis 11: 3182-3189.
Hess, D., Dockalova, V., Kokkonen, P., Bednar, D., Damborsky, J., deMello, A., Prokop, Z., Stavrakis, S., 2021: Exploring Mechanism of Enzyme Catalysis by On-Chip Transient Kinetics Coupled with Global Data Analysis and Molecular Modeling. Chem 7: 1066-1079.
Marques, S. M., Supolikova, L., Molcanova, L., Smejkal, K., Bednar, D., Slaninova, I., 2021: Screening of Natural Compounds as P-Glycoprotein Inhibitors against Multidrug Resistance. Biomedicines 9: 357.
Pinto, G. P., Vavra, O., Marques, S. M., Filipovic, J., Bednar, D., Damborsky, J., 2021: Screening of World Approved Drugs against Highly Dynamical Spike Glycoprotein of SARS-CoV-2 using CaverDock and Machine Learning. Computational and Structural Biotechnology Journal 19: 3187-3197.
Schenkmayerova, A., Pinto, G. P., Toul, M., Marek, M., Hernychova, L., Planas-Iglesias, J., Daniel Liskova, V., Pluskal, D., Vasina, M., Emond, S., Dörr, M., Chaloupkova, R., Bednar, D., Prokop, Z., Hollfelder, F., Bornscheuer, U. T., Damborsky, J., 2021: Engineering the Protein Dynamics of an Ancestral Luciferase. Nature Communications 12: 3616.
Mirela-Bota, P., Aguirre-Plans, J., Meseguer, A., Galletti, C., Segura, J., Planas-Iglesias, J., Garcia-Garcia, J., Guney, E., Oliva, B., Fernandez-Fuentes, N., 2021: Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein-Protein Interaction Data. Journal of Molecular Biology 433: 166656.
Shaposhnikova, A., Kuty, M., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I., Minofar, B., Prudnikova, T., 2021: Stabilization of Haloalkane Dehalogenase Structure by Interfacial Interaction with Ionic Liquids. Crystals 11: 1052.
PDBe-KB consortium, 2021: PDBe-KB: Collaboratively Defining the Biological Context of Structural Data. Nucleic Acids Research gkab988: 1-9.
Markova, K., Kunka, A., Chmelova, K., Havlasek, M., Babkova, P., Marques, S. M., Vasina, M., Planas-Iglesias, J., Chaloupkova, R., Bednar, D., Prokop, Z., Damborsky, J., Marek, M., 2021: Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catalysis 11: 12864-12885.
Brůža, V., Byška, J., Mičan, J. Kozlíková, B., 2021: VRdeo: Creating Engaging Educational Material for Asynchronous Student-teacher Exchange Using Virtual Reality. Computers & Graphics 98: 280-292.
Mazur, A., Grinkevich, P., Chaloupkova, R., Havlickova, P., Kascakova, B., Kuty, M., Damborsky, J., Kuta Smatanova, I., Prudnikova, T., 2021: Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA. International Journal of Molecular Sciences 22: 11992.
Schuiten, E. D., Badenhorst, C. P. S., Palm, G. J., Berndt, L., Lammers, M., Mican, J., Bednar, D., Damborsky, J., Bornscheuer, U. T., 2021: Promiscuous Dehalogenase Activity of the Epoxide Hydrolase CorEH from Corynebacterium sp. C12. ACS Catalysis 11: 6113-6120.
2020
Mazurenko, S., Prokop, Z., Damborsky, J., 2020: Machine Learning in Enzyme Engineering. ACS Catalysis 10: 1210-1223.
Kokkonen, P., Slanska, M., Dockalova, V., Pinto, G. P., Sanchez-Carnerero, E. M., Damborsky, J., Klan, P., Prokop, Z., Bednar, D., 2020: The Impact of Tunnel Mutations on Enzymatic Catalysis Depends on the Tunnel-Substrate Complementarity and the Rate-Limiting Step. Computational and Structural Biotechnology Journal 18: 805-813.
Laham-Karam, N., Pinto, G. P., Poso, A., Kokkonen, P., 2020: Transcription and Translation Inhibitors in Cancer Treatment. Frontiers in Chemistry 8: 276.
Dockalova, V., Sanchez-Carnerero, E. M., Dunajova, Z., Palao, E., Slanska, M., Buryska, T., Damborsky, J., Klan, P., Prokop, Z., 2020: Fluorescent Substrates for Haloalkane Dehalogenases: Novel Probes for Mechanistic Studies and Protein Labeling. Computational and Structural Biotechnology Journal 18: 922-932.
Hon, J., Borko, S., Stourac, J., Prokop, Z., Zendulka, J., Bednar, D., Martinek, T., Damborsky, J., 2020: EnzymeMiner: Automated Mining of Soluble Enzymes with Diverse Structures, Catalytic Properties and Stabilities. Nucleic Acids Research 48: W104–W109.
Chmelova, K., Sebestova, E., Liskova, V., Beier, A., Bednar, D., Prokop Z., Chaloupkova, R., Damborsky, J., 2020: A Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique ( S )-Enantiopreference, and High Thermostability. Applied and Environmental Microbiology 86: e02820-19.
Babkova, P., Dunajova, Z., Chaloupkova, R., Damborsky, J., Bednar. D., Marek, M., 2020: Structures of Hyperstable Ancestral Haloalkane Dehalogenases Show Restricted Conformational Dynamics. Computational and Structural Biotechnology Journal 18: 1497-1508.
Furmanova K., Vavra O., Kozlikova B., Damborsky J., Vonasek V., Bednar D., Byska J., 2020: DockVis: Visual Analysis of Molecular Docking Trajectories. Computer Graphics Forum 39: 452-464.
Mazurenko, S., 2020: Predicting Protein Stability and Solubility Changes Upon Mutations: Data Perspective. ChemCatChem 12: 1-10.
Marek, M., Chaloupkova, R., Prudnikova, T., Sato, Y., Rezacova, P., Nagata, Y., Kuta Smatanova, I., Damborsky, J., 2020: Structural and Catalytic Effects of Surface Loop-helix Transplantation Within Haloalkane Dehalogenase Family. Computational and Structural Biotechnology Journal 18: 1352-1362.
Kumar, L., Planas-Iglesias, J., Harms, C., Kamboj, S., Wright, D., Klein-Seetharaman, J., Sarkar, S. K., 2020: Activity-dependent Interdomain Dynamics of Matrix Metalloprotease-1 on Fibrin. Scientific Reports 10: 1-14.
Stourac, J., Dubrava, J., Musil, M., Horackova, J., Damborsky, J., Mazurenko, S., Bednar, D., 2020: FireProtDB: Database of Manually Curated Protein Stability Data. Nucleic Acids Research 49: D319-D324.
Mazurenko, S., Jauhiainen, J. , Valkonen, T., 2020: Primal-Dual Block-Proximal Splitting for a Class of Non-Convex Problems. Electronic Transactions on Numerical Analysis 52: 509–552.
Markova, K., Chmelova, K., Marques, S. M., Carpentier, P., Bednar. D., Damborsky, J., Marek, M., 2020: Decoding the Intricate Network of Molecular Interactions of a Hyperstable Engineered Biocatalyst. Chemical Science 11: 11162-11178.
Aslan-Uzel, A., Beier, A., Kovar, D., Cziegler, C., Padhi, S. K., Schuiten, E. D., Dorr, M., Böttcher, D., Hollmann, F., Rudroff, F., Mihovilovic, M. D., Buryska, T., Damborsky, J., Prokop, Z., Badenhorst, C. P. S., Bornscheuer, U. T., 2020: An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation. ChemCatChem 12: 2032–2039.
2019
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 W1: W414–W422.
Koledova, Z., Sumbal, J., Rabata, A., La Bourdonnaye, G., Chaloupkova, R., Hrdlickova, B., Damborsky, J., Stepankova, V., 2019: Fibroblast Growth Factor 2 Protein Stability Provides Decreased Dependence on Heparin for Induction of FGFR Signaling and Alters ERK Signaling Dynamics. Frontiers in Cell and Developmental Biology 7: 331.
Demko, M., Chrast, L., Dvorak, P., Damborsky, J., Safranek, D., 2019: Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms 7: 553.
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. Microbial Degradation of Xenobiotics 7: 498.
Byska, J., Trautner, T., Marques S. M., Damborsky, J., Kozlikova, B., Waldner, M., 2019: Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Computer Graphics Forum 38: 441–453.
Cerny, J., Bozikova, P., Balik, A., Marques, S. M., Vyklicky, L., 2019: NMDA Receptor Opening and Closing-Transitions of a Molecular Machine Revealed by Molecular Dynamics. Biomolecules 9: 549.
Pinto, G. P., Vavra, O., Filipovic, J., Stourac, J., Bednar, D., Damborsky, J., 2019: Fast Screening of Inhibitor Binding/Unbinding using Novel Software Tool CaverDock. Frontiers in Chemistry 7: 709.
Prudnikova, T., Kascakova, B., Mesters, J. R., Grinkevich, P., Havlickova, P., Mazur, A., Shaposhnikova, A., Chaloupkova, R., Damborsky, J., Kuty, M., Kuta Smatanova, I., 2019: Crystallization and Crystallographic Characterization of a Bradyrhizobium Elkanii USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site. Crystals 9: 375.
Tratsiak, K., Prudnikova, T., Drienovska, I., Damborsky, J., Brynda, J., Pachl, P., Kuty, M., Chaloupkova, R., Rezacova, P. , Kuta Smatanova, I., 2019: Crystal Structure of the Cold-adapted Haloalkane Dehalogenase DpcA From Psychrobacter Cryohalolentis K5. Acta Crystallographica 75: 324-331.
Kokkonen, P., Bednar, D., Pinto, G., Prokop, Z., Damborsky, J., 2019: Engineering Enzyme Access Tunnels. Biotechnology Advances 37: 107386.
Chaloupkova, R., Liskova, V., Toul, M., Markova, K., Sebestova, E, Hernychova, L., Marek, M. Pinto. G. P., Pluskal, D., Waterman, J., Prokop, Z., Damborsky, J., 2019: Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts. ACS Catalysis 9: 4810–4823.
Vavra, O., Filipovic, J., Plhak, J., Bednar, D., Marques, S.M., 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.
Buryska, T., Vasina, M., Gielen, F., Vanacek, P., van Vliet, L., Jezek, J., Pilat, Z., Zemanek, P., Damborsky, J., Hollfelder, F., Prokop, Z., 2019: Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics. Analytical Chemistry 91: 10008-10015.
Beier, A., Damborsky, J., Prokop, Z, 2019: Transhalogenation Catalysed by Haloalkane Dehalogenases Engineered to Stop Natural Pathway at Intermediate. Advanced Synthesis & Catalysis 11: 2438-2442.
Mican, J., Toul, M., Bednar, D., Damborsky, J., 2019: Structural Biology and Protein Engineering of Thrombolytics. Computational and Structural Biotechnology Journal 17: 917-938.
Filipovic, J., Vavra, O., Plhak, J., Bednar, D., Marques, S., Brezovsky, J., Matyska, L., Damborsky, J., 2019: CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE/ACM Transactions on Computational Biology and Bioinformatics 17: 1625-1638.
Horvath,, P., Sebej, P., Kovar, D., Damborsky, J., Prokop, Z., Klan, P., 2019: Fluorescent pH Indicators for Neutral to Near-Alkaline Conditions Based on 9‑Iminopyronin Derivatives. ACS Omega 4: 5479−5485.
Nevolova, S., Manaskova, E., Mazurenko, S., Damborsky, J., Prokop, Z., 2019: Development of Fluorescent Assay for Monitoring of Dehalogenase Activity. Biotechnology Journal 14: e1800144.
Marques, S. M., Bednar, D., Damborsky, J., 2019: Computational Study of Protein-Ligand Unbinding for Enzyme Engineering. Frontiers in Chemistry 6: 650.
Musil, M., Konegger, H., Hon, J., Bednar, D., Damborsky, J., 2019: Computational Design of Stable and Soluble Biocatalysts. ACS Catalysis 9: 1033−1054.
Jindal, G., Slanska, K., Kolev, V., Damborsky, J., Prokop, Z., Warshel, A., 2019: Exploring the Challenges of Computational Enzyme Design by Rebuilding the Active Site of a Dehalogenase. Proceedings of the National Academy of Sciences of the United States of America 116: 389–394.
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.
Pilat, Z., Kizovsky, M., Jezek, J., Kratky, S., Sobota, J., Siler, M., Samek, O., Buryska, T., Vanacek, P., Damborsky, J., Prokop, Z., Zemanek, P., 2018: Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips. Sensors 18: 3212.
Beerens, K., Mazurenko, S., Kunka, A., Marques, S. M., 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.
Kokkonen, P., Bednar, D., Dockalova, V., Prokop, Z., Damborsky, J., 2018: Conformational Changes Allow Processing of Bulky Substrates by a Haloalkane Dehalogenase with a Small and Buried Active Site. The Journal of Biological Chemistry 29: 11505-11512.
Mazurenko, S., 2018: Viscosity Solutions to Evolution Problems of Star-Shaped Reachable Sets. Nonlinear Differential Equations and Applications NoDEA 25: 29.
Mazurenko, S., Stourac, J., Kunka, A., Nedejlkovic, S., Bednar, D., Prokop, Z., Damborsky, J., 2018: CalFitter: A Web Server for Analysis of Protein Thermal Denaturation Data. Nucleic Acids Research 46: W344-W349.
Sumbalova, L., Stourac, J., Martinek, T., Bednar, D., Damborsky, J., 2018: HotSpot Wizard 3.0: Web Server for Automated Design of Mutations and Smart Libraries Based on Sequence Input Information. Nucleic Acids Research 46: W356-W362.
Mazurenko, S., Bidmanova, S., Kotlanova, M., Damborsky, J., Prokop, Z., 2018: Sensitive Operation of Enzyme-based Biodevices by Advanced Signal Processing. PLOS One 13: e0198913.
Kunka, A., Damborsky, J., Prokop, Z., 2018: Haloalkane Dehalogenases from Marine Organisms. Methods in Enzymology 605: 203-251.
Jurcik, A., Bednar, D., Byska, J., Marques, S. M., 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.
Kaushik, S., Marques, S. M., 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.
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., Dambor, 2018: Computer-Assisted Engineering of Hyperstable Fibroblast Growth Factor 2. Biotechnology and Bioengineering 115: 850-862.
Chrast, L., Chaloupkova, R., Damborsky, J., 2018: Gram-scale Production of Recombinant Microbial Enzymes in Shake Flasks. FEMS Microbiology Letters 365: fnx265.
Buryska, T., Babkova, P., Vavra, O., Damborsky, J., Prokop, Z., 2018: A Haloalkane Dehalogenase From a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity. Applied and Environmental Microbiology 84: e01684-17.
2017
Mazurenko, S., Kunka, A., Beerens, K., Johnson, C. M., Damborsky, J., Prokop, Z., 2017: Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating. Scientific Reports 7: 16321.
Marques, S. M., Dunajova, Z., Prokop, Z., Chaloupkova, R., Brezovsky, J., Damborsky, J., 2017: Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling. Journal of Chemical Information and Modeling 57: 1970-1989.
Valuchova, S., Fulnecek, J., Prokop, Z., Stolt-Bergner, P., Janouskova, E., Hofr, C., Riha, K., 2017: Protection of Arabidopsis Blunt-Ended Telomeres is Mediated by a Physical Association with the Ku Heterodimer. The Plant Cell Online 29: 1533-1545.
Dvorak, P., Nikel, P.I., Damborsky, J., de Lorenzo, V., 2017: Bioremediation 3.0: Engineering Pollutant-Removing Bacteria in the Times of Systemic Biology. Biotechnology Advances 7: 845-866.
Vad, V. , Byska, J., Jurcik, A., Viola, I. , Groller, E. M., Hauser, H., Marques, S. M., Damborsky, J., Kozlikova, B., 2017: Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. Eurographics Workshop on Visual Computing for Biology and Medicine Proceedings 36: 33-42.
Kotik, M., Vanacek, P., Kunka, A., Prokop, Z., Damborsky, J., 2017: Metagenome-derived Haloalkane Dehalogenases with Novel Catalytic Properties. Applied Microbiology and Biotechnology 101: 6385-6397.
Schwarte, A., Genz, M., Skalden, L., Nobili, A., Vickers, C., Melse, O., Kuipers, R., Joosten, H., Stourac, J., Bendl, J., Black, J., Haase, P., Baakman, C, Damborsky, J., Bornscheuer, U, Vriend, G., Venselaar, H., 2017: NewProt – a Protein Engineering Portal. Protein Engineering, Design & Selection 30: 441-447.
Babkova, P., Sebestova, E., Brezovsky, J., Chaloupkova, R., Damborsky, J., 2017: Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity. ChemBioChem 18: 1448-1456.
Marques, S. M., 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.
Nehybova T., Smarda, J., Daniel, L., Stiborek, M., Kanicky, V., Spasojevic, I., Preisler, J., Damborsky, J., Benes, P, 2017: Wedelolactone Acts as Proteasome Inhibitor in Breast Cancer Cells. International Journal of Molecular Sciences 18: E729.
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.
Musil, M., Stourac, J., Bendl, J., Brezovský, 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 (W1): W393-W399.
Kaushik, S., Prokop, Z., Damborsky, J., Chaloupkova, R., 2017: Kinetics of Binding of Fluorescent Ligands to Enzymes with Engineered Access Tunnels. FEBS Journal 284: 134-148.
2016
Artaza, H., Chue Hong, N., Corpas, M., Corpuz, A., Hooft, R., Jiménez, R. C., Leskošek, B., Olivier, B. G., Stourac, J., Svobodová Vařeková, R., Van Parys, T., Vaughan, D., 2016: Top 10 Metrics for Life Science Software Good Practices. F1000Research 2016 5: 2000.
Gloser, V., Korovetska, H., Martin-Vertedor, A. I., Hajickova, M., Prokop, Z., Wilkinson, S., Davies, W., 2016: The Dynamics of Xylem Sap pH under Drought: a Universal Response in Herbs?. Plant and Soil 409: 259-272.
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.
Gross, J., Prokop, Z., Janssen, D., Faber, K., Hall, M., 2016: Regio- and Enantioselective Sequential Dehalogenation of rac-1,3-Dibromobutane by Haloalkane Dehalogenase LinB. ChemBioChem 17: 1437-1441.
Krauskova, L., Prochazkova, J., Klaskova, M., Filipova, L., Chaloupkova, R., Maly, S., Damborsky, J., Heger, D., 2016: Suppression of Protein Inactivation During Freezing by Minimizing pH Changes Using Ionic Cryoprotectants. International Journal of Pharmaceutics 509: 41-49.
Pavelka, A., Sebestova, E., Kozlikova, B., Brezovsky, J., Sochor, J., Damborsky, J., 2016: CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13: 505-517.
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.
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-W487.
Bidmanova, S., Steiner, M.S., Stepan, M., Vymazalova, K., Gruber, M.A., Duerkop, A., Damborsky, J., Prokop, Z., Wolfbeis, O.S., 2016: Enzyme Based Test Stripes for the Visual or Photographic Detection and Quantitation of Gaseous Sulfur Mustard. Analytical Chemistry 88: 6044-6049.
Mazurenko, S., 2016: Partial Differential Equation for Evolution of Star-Shaped Reachability Domains of Differential Inclusions. Set-Valued and Variational Analysis 24: 333-354.
Krupka, M., Masek, J., Barkocziova, L., Turanek Knotigova, P., Kulich, P., Plockova, J., Lukac, R., Bartheldyova, E., Koudelka, S., Chaloupkova, R., Sebela, M., Zyka, D., Droz, L., Effenberg, R., Ledvina, M., Miller, A.D., Turanek, J., Raska, M., 2016: The Position of His-Tag in Recombinant OspC and Application of Various Adjuvants Affects the Intensity and Quality of Specific Antibody Response after Immunization of Experimental Mice. PLOS One 11: e0148497.
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.
Bidmanova, S., Kotlanova, M., Rataj, T., Damborsky, J., Trtilek, M., Prokop, Z., 2016: Fluorescence-Based Biosensor for Monitoring of Environmental Pollutants: From Concept to Field Application. Biosensors and Bioelectronics 84: 97-105.
Prokop, Z., Necasova, A., Klanova, J., Cupr, P., 2016: Bioavailability and Mobility of Organic Contaminants in Soil: New Three-Step Ecotoxicological Evaluation. Environmental Science and Pollution Research 23: 4312-4319.
Ison, J., Rapacki, K., Ménager, H., Kalaš, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G.D., Dog, 2016: Tools and Data Services Registry: a Community Effort to Document Bioinformatics Resources. Nucleic Acids Research 44: D38-47.
2015
Dvorak, P., Chrast, L., Nikel, P.I., Fedr, R., Soucek, K., Sedlackova, M., Chaloupkova, R., de Lorenzo, V., Prokop, Z., Damborsky, J., 2015: Exacerbation of Substrate Toxicity by IPTG in Escherichia coli BL21(DE3) Carrying a Synthetic Metabolic Pathway. Microbial Cell Factories 14: 201.
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.
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.
Shrivastava, N., Prokop, Z., Kumar, A., 2015: Novel LinA Type 3 δ-Hexachlorocyclohexane Dehydrochlorinase. Applied and Environmental Microbiology 81: 7553-7559.
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.
Amaro, M., Brezovsky, J., Kovacova, S., Sykora, J., Bednar, D., Nemec, V., Liskova, V., Kurumbang, N., 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.
Buchtova, M., Chaloupkova, R., Zakrzewska, M., Vesela, I., Cela, P., Barathova, J., Gudernova, I., Zajickova, R., Trantirek, L., Martin, J., Kostas, M., Otlewski, J., Damborsky, J., Kozubik, A., Wiedlocha, A., Krejci, P., 2015: Instability Restricts Signaling of Multiple Fibroblast Growth Factors. Cellular and Molecular Life Sciences 72: 2445-2459.
Liskova, V., Bednar, D., 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.
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.
Gielen, F., Buryska, T., Butz, M., van Vliet, L., Damborsky, J., Prokop, Z., Hollfelder, F., 2015: Interfacing Microwells with Nanoliter Compartments: A Sampler Generating High-Resolution Concentration Gradients for Quantitative Biochemical Analyses in Droplets. Analytical Chemistry 87: 624-632.
2014
Sebestova, E., Bendl, J., Brezovsky, J., Damborsky, J., 2014: Computational Tools for Designing Smart Libraries. Methods in Molecular Biology 1179: 291-314.
Vymetal, J., Bathula, S. R., Cerny, J., Chaloupkova, R., Zidek, L., Sklenar, V., Vondrasek, J., 2014: Retro Operation on the Trp-Cage Miniprotein Sequence Produces an Unstructured Molecule Capable of Folding Similar to the Original Only upon 2,2,2-Trifluoroethanol Addition. Protein Engineering, Design & Selection 27: 463-472.
Moriuchi, R., Tanaka, H., Nikawadori, Y., Ishitsuka, M., Ito, M., Ohtsubo, Y., Tsuda, M., Damborsky, J., Prokop, Z., Nagata, Y., 2014: Stepwise Enhancement of Catalytic Performance of Haloalkane Dehalogenase LinB towards β-Hexachlorocyclohexane. Applied Microbiology and Biotechnology Express 4: 72.
Ghufrana, S., Pavlova, M., Arif, M.I., Postema, C.P., Damborsky, J., Janssen, D.B., 2014: A Pseudomonas putida Strain Genetically Engineered for 1,2,3-Trichloropropane Bioremediation. Applied and Environmental Microbiology 80: 5467-5476.
Dvorak, P., Kurumbang, N.P., Bendl, J., Brezovsky, J., Prokop, Z., Damborsky, J., 2014: Maximizing the Efficiency of Multi-enzyme Process by Stoichiometry Optimization. ChemBioChem 15: 1891-1895.
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.
Dvorak, P., Bidmanova, S., Damborsky, J., Prokop, Z., 2014: Immobilized Synthetic Pathway for Biodegradation of Toxic Recalcitrant Pollutant 1,2,3-Trichloropropane. Environmental Science & Technology 48: 6859-6866.
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 D70: 1884-1897.
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.
Bidmanova, S., Hrdlickova, E., Jaros, J., Ilkovics, L., Hampl, A., Damborsky, J., Prokop, Z., 2014: Microscopic Monitoring Provides Information on Structure and Properties During Biocatalyst Immobilisation. Biotechnology Journal 9: 852-860.
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.
Stepankova, V., Vanacek, P., Damborsky, J., Chaloupkova, R., 2014: Comparison of Catalysis by Haloalkane Dehalogenases in Aqueous Solutions of a Deep Eutectic and Organic Solvents. Green Chemistry 16: 2754-2761.
Bendl J., Stourac J., Salanda O., Pavelka A., Wieben E.D., Zendulka J., Brezovsky J., Damborsky J., 2014: PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations. PLOS Computational Biology 10: e1003440.
Kurumbang, N.P., 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.
Damborsky, J., Brezovsky, J., 2014: Computational Tools for Designing and Engineering Enzymes. Current Opinion in Chemical Biology 19: 8-16.
Lahoda, M., Mesters, J. R., Stsiapanava, A., Chaloupkova, R., Kuty, M., Damborsky, J., Kuta Smatanova, I., 2014: Crystallographic Analysis of 1,2,3-Trichloropropane Biodegradation by Haloalkane Dehalogenase DhaA31. Acta Crystallographica D70: 209-217.
2013
Burgess, R.C., Sebesta, M., Sisakova, A., Marini, V.P., Lisby, M., Damborsky, J., Klein, H., Rothstein, R., Krejci, L., 2013: The PCNA Interaction Protein Box in Rad54 is an Integral Part of Its ATPase Domain and is Required for Efficient DNA Repair and Recombination. PLOS ONE 8: e82630.
Novotna, J., Olsovska, J., Novak, P., Mojzes, P., Chaloupkova, R., Kamenik, Z., Spizek, J., Kutejova, E., Mareckova, M., Tichy, P., Damborsky, J., Janata, J., 2013: Lincomycin Biosynthesis Involves a Tyrosine Hydroxylating Heme Protein of an Unusual Enzyme Family. PLOS ONE 8: e79974.
Stepankova, V., Bidmanova, S., Koudelakova, T., Prokop, Z., Chaloupkova, R., Damborsky, J., 2013: Strategies for Stabilization and Activation of Biocatalysts in Organic Solvents. ACS Catalysis 3: 2823-2836.
Hladilkova, J., Prokop, Z., Chaloupkova, R., Damborsky, J., Jungwirth, P., 2013: Release of Halide Ions from the Buried Active Site of the Haloalkane Dehalogenase LinB Revealed by Stopped-Flow Fluorescence Analysis and Free Energy Calculations. Journal of Physical Chemistry B 117: 14329-14335.
Fortova, A., Sebestova, E., Stepankova, V., Koudelakova, T., Palkova, L., Damborsky, J., Chaloupkova, R., 2013: DspA from Strongylocentrotus purpuratus: the First Biochemically Characterized Haloalkane Dehalogenase of Non-Microbial Origin. Biochimie 95: 2091-2096.
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.
Tratsiak, K., Degtjarik, O., Drienovska, I., Chrast, L., Rezacova, P., Kuty, M., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I., 2013: Crystallographic Analysis of New Psychrophilic Haloalkane Dehalogenases: DpcA from Psychrobacter cryohalolentis K5 and DmxA from Marinobacter sp. ELB17. Acta Crystallographica F69: 683-688.
Stepankova, V., Paterova, J., Damborsky, J., Jungwirth, P., Chaloupkova, R., Heyda, J., 2013: Cation-Specific Effects on Enzymatic Catalysis Driven by Interactions at the Tunnel Mouth. Journal of Physical Chemistry B 117: 6394-6402.
Gora, A., Brezovsky, J., Damborsky, J., 2013: Gates of Enzymes. Chemical Reviews 113: 5871–5923.
Bidmanova, S., Damborsky, J., Prokop, Z., 2013: Immobilization of Haloalkane Dehalogenase LinB from Sphingobium japonicum UT26 for Biotechnological Applications. Journal of Biocatalysis & Biotransformation 2: 1-7.
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.
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.
Stepankova, V., Damborsky, J., Chaloupkova, R., 2013: Organic Co-solvents Affect Activity, Stability and Enantioselectivity of Haloalkane Dehalogenases. Biotechnology Journal 8: 719-729.
Degtjarik, O., Chaloupkova, R., Rezacova, P., Kuty, M., Damborsky, J., Kuta Smatanova, I., 2013: Differences in crystallization of two LinB variants from Sphingobium japonicum UT26. Acta Crystallographica F69: 284-287.
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.
Koudelakova, T., Bidmanova, T., Dvorak, P., Pavelka, A., Chaloupkova, R., Prokop, Z., Damborsky, J., 2013: Haloalkane Dehalogenases: Biotechnological Applications. Biotechnology Journal 8: 32-45.
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, U. T., 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.
Niharika, N., Moskalikova, H., Kaur, J., Khan, F., Sedlackova, M., Hampl, A., Damborsky, J., Prokop, Z., Lal, R., 2013: Sphingobium czechense sp. nov., Isolated from a Hexachlorocyclohexane (HCH) Dump Site. International Journal of Systematic and Evolutionary Microbiology 63: 673-678.
Niharika, N., Moskalikova, H., Kaur, J., Sedlackova, M., Hampl, A., Damborsky, J., Prokop, Z., Lal, R., 2013: Novosphingobium barchaimii sp. nov., Isolated from a Hexachlorocyclohexane (HCH) Contaminated Soil. International Journal of Systematic and Evolutionary Microbiology 63: 667-672.
Kaur, J., Moskalikova, H., Niharika, N., Sedlackova, M., Hampl, A., Damborsky, J., Prokop, Z., Lal, R., 2013: Sphingobium baderi sp. nov., Isolated from a Hexachlorocyclohexane (HCH) Dump Site in Spolana. International Journal of Systematic and Evolutionary Microbiology 63: 723-728.
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.
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.
Biedermannova, L., Prokop, Z., Gora, A., Chovancova, E., Kovacs, M., Damborsky, J., Wade, R.C., 2012: A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB. The Journal of Biological Chemistry 287: 29062-29074.
Drienovska, I., Chovancova, E., Koudelakova, T., Damborsky, J., Chaloupkova, R., 2012: Biochemical Characterization of a Novel Haloalkane Dehalogenase from a Cold-Adapted Bacterium. Applied and Environmental Microbiology 78: 4995-4998.
Balonova, L., Mann, B.F., Cerveny, L., Alley, W.R., Chovancova, E., Forslund, A.-L., Salomonsson, E.N., Forsberg, Å., Damborsky, J., Novotny, M.V., Hernychova, L., Stulik, J., 2012: Characterization of Protein Glycosylation in Francisella tularensis subsp. holarctica; Identification of a Novel Glycosylated Lipoprotein Required for Virulence. Molecular & Cellular Proteomics 11: M111.015016.
Dokladal, L., Oboril, M., Zdrahal, Z., Ptackova, N., Chaloupkova, R., Damborsky, J., Kasparovsky, T., Jeandroz, S., Lochman, J., 2012: Physiological and Proteomic Approaches to Evaluate the Role of Sterol Binding in Elicitin-Induced Resistance. Journal of Experimental Botany 63: 2203-2215.
Bidmanova, S., Hlavacek, A., Damborsky, J., Prokop, Z., 2012: Conjugation of 5(6)-Carboxyfluorescein and 5(6)-Carboxynaphthofluorescein with Bovine Serum Albumin and Their Immobilization for Optical pH Sensing. Sensors and Actuators B: Chemical 161: 93-99.
2011
Stsiapanava A, Dohnalek J, Gavira JA, Kuty M, Koudelakova T, Damborsky J, Kuta Smatanova I., 2011: Atomic Resolution Studies of Haloalkane Dehalogenases DhaA04, DhaA14 and DhaA15 with Engineered Access Tunnels. Acta crystallographica. Section D, Biological crystallography 66: 962-969.
Bouchal, P., Jarkovsky, J., Hrazdilova, K., Mudrochova, M., Struharova, I., Hernychova, L., Damborsky, J., Sova, P., Vojtesek, B., 2011: The New Platinum-Based Anticancer Agent LA12 Induces Retinol Binding Protein 4 In Vivo. Proteome Science 9: 68-77.
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.
Chaloupkova, R., Prokop, Z., Sato, Y., Nagata, Y., Damborsky, J., 2011: Stereoselectivity and Conformational Stability of Haloalkane Dehalogenase DbjA from Bradyrhizobium japonicum USDA110: The Effect of pH and Temperature. FEBS Journal 278: 2728-2738.
Pleskova, V., Kasparovsky, T., Oboril, M., Ptackova, N., Chaloupkova, R., Dokladal, L., Damborsky, J., Lochman, J., 2011: Elicitin–membrane Interaction Is Driven By a Positive Charge on the Protein Surface: Role of Lys13 Residue in Lipids Loading and Resistance Induction. Plant Physiology and Biochemistry 49: 321-328.
Prudnikova, T., Chaloupkova, R., Sato, Y., Nagata, Y., Degtjarik, O., Kuty, M., Rezacova, P., Damborsky, J., Kuta Smatanova, I., 2011: Development of a Crystallization Protocol for the DbeA1 Variant of Novel Haloalkane Dehalogenase from Bradyrhizobium elkani USDA94. Crystal Growth & Design 11: 516-519.
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.
Stsiapanava, A., Chaloupkova, R., Fortova, A., Brynda, J., Weiss, M. S., Damborsky, J., Kuta Smatanova, I., 2011: Crystallization and Preliminary X-ray Diffraction Analysis of the Wild-Type Haloalkane Dehalogenase DhaA and its Variant DhaA13 Complexed with Different Ligands. Acta Crystallographica F67: 253-257.
Hasan, K., Fortova, A., Koudelakova, T., Chaloupkova, R., Ishitsuka, M., Nagata, Y., Damborsky, J., Prokop, Z., 2011: Biochemical Characteristics of the Novel Haloalkane Dehalogenase DatA Isolated from the Plant Pathogen Agrobacterium tumefaciens C58. Applied and Environmental Microbiology 77: 1881-1884.
Lahoda, M., Chaloupkova, R., Stsiapanava, A., Damborsky, J., Kuta Smatanova, I., 2011: Crystallization and Crystallographic Analysis of the Rhodococcus rhodochrous NCIMB 13064 DhaA Mutant DhaA31 and its Complex with 1,2,3-Trichloropropane. Acta Crystallographica F67: 397-400.
2010
Literakova, P., Lochman, J., Zdrahal, Z., Prokop, Z., Mikes, V., Kasparovsky, T., 2010: Determination of Capsidiol in Tobacco Cells Culture by HPLC. Journal of Chromatographic Science 48: 436-440.
Vejvoda, V., Kubac, D., Davidova, A., Kaplan, O., Sulc, M., Sveda, O., Chaloupkova, R., Martinkova, L., 2010: Purification and Characterization of Nitrilase from Fusarium solani IMI196840. Process Biochemistry 45: 1115-1120.
Martins dos Santos, V.A.P., Damborsky, J., 2010: Systems Biology at Work. Current Opinion in Biotechnology 21: 498-501.
Altmannova, V., Eckert-Boulet, N., Arneric, M., Kolesar, P., Chaloupkova, R., Damborsky, J., Sung, P., Zhao, X., Lisby, M., Krejci, L., 2010: Rad52 SUMOylation Affects the Efficiency of the DNA Repair. Nucleic Acids Research 38: 4708-4721.
Bidmanova, S., Chaloupkova, R., Damborsky, J., Prokop, Z., 2010: Development of an Enzymatic Fiber-Optic Biosensor for Detection of Halogenated Hydrocarbons. Analytical and Bioanalytical Chemistry 398: 1891-1898.
Stsiapanava, A., Dohnalek, J., Gavira, J., A., Kuty, M., Koudelakova, T., Damborsky, J., Kuta Smatanova, I., 2010: Atomic Resolution Studies of Haloalkane Dehalogenases DhaA04, DhaA14 and DhaA15 with Engineered Access Tunnels. Acta Crystallographica D66: 962-969.
Prokop, Z., Sato, Y., Brezovsky, J., Mozga, T., Chaloupkova, R., Koudelakova, T., Jerabek, P., Stepankova, V., Natsume, R., Leeuwen, J. G. E., Janssen, D. B., 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.
Bidmanova, S., Pohanka, M., Cabal, J., Prokop, Z., Damborsky, J., 2010: Early Warning Biosensors for Detection of Chemical Warfare Agents. Chemicke Listy 104: 302-308.
Malcikova, J., Tichy, B., Damborsky, J., Kabathova, J., Trbusek, M., Mayer, J., Pospisilova, S., 2010: Analysis of the DNA-Binding Activity of p53 Mutants Using Functional Protein Microarrays and its Relationship to Transcriptional Activation. Biological Chemistry 391: 197-205.
2009
Mozga, T., Prokop, Z., Chaloupkova, R., Damborsky, J., 2009: Chiral Aliphatic Hydroxy Compounds in Nature: a Review of Biological Functions and Practical Applications. Collection of Czechoslovak Chemical Communications 74: 1195-1278.
Klvana, M., Pavlova, M., Koudelakova, T., Chaloupkova, R., Dvorak, P., Prokop, Z., Stsiapanava, A., Kuty, M., Kuta Smatanova, I., Dohnalek, J., Kulhanek, P., Wade, R.C., Damborsky, J., 2009: Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. Journal of Molecular Biology 392: 1339-1356.
Macek, P., Chmelik, J., Krizova, I., Kaderavek, P., Padrta, P., Zidek, L., Wildova, M., Hadravova, R., Chaloupkova, R., Pichova, I., Ruml, T., Rumlova, M., Sklenar, V., 2009: NMR Structure of the N-Terminal Domain of Capsid Protein from the Mason–Pfizer Monkey Virus. Journal of Molecular Biology 392: 100-114.
Pavlova, M., Klvana, M., Prokop, Z., Chaloupkova, R., Banas, P., Otyepka, M., Wade, R., Nagata, Y., Damborsky, J., 2009: Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate. Nature Chemical Biology 5: 727-733.
Jesenska, A., Monincova, M., Koudelakova, T., Hasan, K., Chaloupkova, R., Prokop, Z., Geerlof, A., Damborsky, J., 2009: Isolation and Biochemical Characterization of Haloalkane Dehalogenases DrbA and DmbC: Representatives of Novel Subfamily. Applied and Environmental Microbiology 75: 5157-5160.
Pavelka, A., Chovancova, E., Damborsky, J., 2009: HotSpot Wizard: a Web Server for Identification of Hot Spots in Protein Engineering. Nucleic Acids Research 37: W376-W383.
Damborsky, J., 2009: Editorial: Protein Design and Engineering for Biocatalysis. Biotechnology Journal 4: 439.
Prudnikova, T., Mozga, T., Rezacova, P., Chaloupkova, R., Sato, Y., Nagata, Y., Brynda, J., Kuty, M., Damborsky, J., Kuta Smatanova, I., 2009: Crystallization and Preliminary X-ray Analysis of a Novel Haloalkane Dehalogenase DbeA from Bradyrhizobium elkani USDA94. Acta Crystallographica F65: 353-356.
Damborsky, J., Brezovsky, J., 2009: Computational Tools for Designing and Engineering Biocatalysts. Current Opinion in Chemical Biology 13: 26-34.
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.
2008
Dopitova, R., Mazura, P., Janda, L., Chaloupkova, R., Jerabek, P., Damborsky, J., Kiran, N., S., Brzobohaty, B., 2008: Functional analysis of the aglycone-binding site of the maize β-glucosidase Zm-p60.1. FEBS Journal 275: 6123-6135.
Mikelova, R., Prokop, Z., Stejskal, K., Adam, V., Beklova, M., Trnkova, L., Kulichova, B., Horna, A., Chaloupkova, R., Damborsky, J., Kizek, R., 2008: Enzymatic Reaction Coupled with Flow-Injection Analysis with Charged Aerosol, Coulometric, or Amperometric Detection for Estimation of Contamination of the Environment by Pesticides. Chromatographia 67: S47-S53.
Grochova, D., Vankova, J., Damborsky, J., Ravcukova, B., Smarda, J., Vojtesek, B., Smardova, J., 2008: Analysis of Transactivation Capability and Conformation of p53 Temperature-Dependent Mutants and their Reactivation by Amifostine in Yeast. Oncogene 27: 1243-1252.
Otyepka, M., Banas, P., Magistrato, A., Carloni, P., Damborsky, J., 2008: Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods. Proteins 70: 707-717.
Stsiapanava, A., Koudelakova, T., Lapkouski, M., Pavlova, M., Damborsky, J., Kuta Smatanova, I., 2008: Crystals of DhaA Mutants from Rhodococcus rhodochrous NCIMB 13064 Diffracted to Ultrahigh Resolution: Crystallization and Preliminary Diffraction Analysis. Acta Crystallographica F64: 137-140.
2007
Chovancova, E., Kosinski, J., Bujnicki, J.M., Damborsky, J., 2007: Phylogenetic Analysis of Haloalkane Dehalogenases. Proteins 67: 305-316.
Pavlova, M., Klvana, M., Jesenska, A., Prokop, Z., Konecna, H., Sato, T., Tsuda, M., Nagata, Y., Damborsky, J., 2007: The Identification of Catalytic Pentad in the Haloalkane Dehalogenase DhmA from Mycobacterium avium N85: Reaction Mechanism and Molecular Evolution. Journal of Structural Biology 157: 384-392.
Chroust, K., Pavlova, M., Prokop, Z., Mendel, J., Bozkova, K., Kubat, Z., Zajickova, V., Damborsky, J., 2007: Quantitative Structure-Activity Relationships for Toxicity and Genotoxicity of Halogenated Aliphatic Compounds: Wing Spot Test of Drosophila melanogaster. Chemosphere 67: 152-159.
Damborsky, J., 2007: Meeting Report: Protein Design and Evolution for Biocatalysis. Biotechnology Journal 2: 176-179.
Damborsky, J., Petrek, M., Banas, P., Otyepka, M., 2007: Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles. Biotechnology Journal 2: 62-67.
Vasickova, P., Machackova, E., Lukesova, M., Damborsky, J., Horky, O., Pavlu, H., Kuklova, J., Kosinova, V., Navratilova, M., Foretova, L., 2007: High Occurrence of BRCA1 Intragenic Rearrangements in Hereditary Breast and Ovarian Cancer Syndrome in the Czech Republic. BMC Medical Genetics 8: 32.
Ito, M., Prokop, Z., Klvana, M., Otsubo, Y., Tsuda, M., Damborsky, J., Nagata, Y., 2007: Degradation of Beta-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Hexachlorocyclohexane-Utilizing Bacterium Sphingobium sp. MI1205. Archives of Microbiology 188: 313-325.
Negri, A., Marco, E., Damborsky J., Gago, F., 2007: Stepwise Dissection and Visualization of the Catalytic Mechanism of Haloalkane Dehalogenase LinB using Molecular Dynamics Simulations and Computer Graphics. Journal of Molecular Graphics and Modelling 26: 643-651.
Vacek, J., Mozga, T., Cahova, K., Pivonkova, H., Fojta, M., 2007: Electrochemical Sensing of Chromium-Induced DNA Damage: DNA Strand Breakage by Intermediates of Chromium(VI) Electrochemical Reduction. Electroanalysis 19: 2093-2102.
Silberstein, M., Damborsky, J., Vajda, S., 2007: Exploring the Binding Sites of the Haloalkane Dehalogenase DhlA from Xanthobacter autotrophicus GJ10. Biochemistry 46: 9239-9249.
Sato, Y., Natsume, R., Tsuda, M., Damborsky, J., Nagata, Y., Senda, T., 2007: Crystallization and Preliminary Crystallographic Analysis of a Haloalkane Dehalogenase DbjA from Bradyrhizobium japonicum USDA110. Acta Crystallographica Section F 63: 294-296.
Monincova, M., Prokop, Z., Vevodova, J., Nagata, Y., Damborsky, J., 2007: Weak Activity of Haloalkane Dehalogenase LinB with 1,2,3-Trichloropropane Revealed by X-ray Crystallography and Microcalorimetry. Applied and Environmental Microbiology 73: 2005-2008.
2006
Prokop, Z., Oplustil, F., DeFrank, J., Damborsky, J., 2006: Enzymes Fight Chemical Weapons. Biotechnology Journal 1: 1370-1380.
Papezova K., Nemec T., Chaloupkova R., Glatz Z., 2006: Study of Substrate Inhibition by Electrophoretically Mediated Microanalysis in Partially Filled Capillary. Journal of Chromatography A 1150: 327-331.
Banas, P., Otyepka, M., Jerabek, P., Petrek, M., Damborsky, J., 2006: Mechanism of Enhanced Conversion of 1,2,3-Trichloropropane by Mutant Haloalkane Dehalogenase Revealed by Molecular Modeling. Journal of Computer-Aided Molecular Design 20: 375-383.
Petrek, M., Otyepka, M., Banas, P., Kosinova, P., Koca, J., Damborsky, J., 2006: CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities. BMC Bioinformatics 7: 316.
Damborsky, J., Prokop, Z., Kostka, M., 2006: Perspectives: Biotechnology in Czech Republic, the Past and the Future. Biotechnology Journal 1: 487-490.
Tvrzova, L., Prokop, Z., Navratilova, J., Mullerova, R., Neca, J., 2006: Development of a Microtiter Plate-Based Method for Determination of Degradation Profile of Nitrophenolic Compounds. Journal of Microbiological Methods 65: 551-556.
Nakamura, T., Zamocky, M., Zdrahal, Z., Chaloupkova, R., Monincova, M., Prokop, Z., Nagata, Y., Damborsky, J., 2006: Expression of Glycosylated Haloalkane Dehalogenase LinB in Pichia pastoris. Protein Expression and Purification 46: 85-91.
2005
Jesenska, A., Pavlova, M., Strouhal, M., Chaloupkova, R., Tesinska, I., Monincova, M., Prokop, Z., Bartos, M., Pavlik, I., Rychlik, I., Mobius, P., Nagata, Y., Damborsky, J., 2005: Cloning, Biochemical Properties, and Distribution of Mycobacterial Haloalkane Dehalogenases. Applied and Environmental Microbiology 71: 6736-6745.
Sato, Y., Monincova, M., Chaloupkova, R., Prokop, Z., Ohtsubo, Y., Minamisawa, K., Tsuda, M., Damborsky, J., Nagata, Y., 2005: Two Rhizobial Strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, Encode Haloalkane Dehalogenases with Novel Structures and Substrate Specificities. Applied and Environmental Microbiology 71: 4372-4379.
Lochman, J., Kasparovsky, T., Damborsky, J., Osman, H., Marais, A., Chaloupkova, R., Ponchet, M., Blein, J.-P., Mikes, V., 2005: Construction of Cryptogein Mutants, Proteinaceous Elicitor from Phytophthora, with Altered Abilities to Induce Defense Reaction in Tobacco Cells. Biochemistry 44: 6565-6572.
Nagata, Y., Prokop, Z., Sato, Y., Jerabek, P., Kumar, A., Ohtsubo, Y., Tsuda, M., Damborsky, J., 2005: Degradation of b-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26. Applied and Environmental Microbiology 71: 2183-2185.
Kmunicek, J., Hynkova, K., Jedlicka, T., Nagata, Y., Negri, A., Gago, F., Wade, R.C., Damborsky, J., 2005: Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26. Biochemistry 44: 3390-3401.
2004
Dobes, P., Kmunicek, J., Mikes, V., Damborsky, J., 2004: Binding of Fatty Acids to b-Cryptogein: Quantitative Structure-Activity Relationships and Design of Selective Protein Mutants. Journal of Chemical Information and Modeling 44: 2126-2132.
Eriksson, L., Damborsky, J., Earll, M., Johansson, E., Trygg, J., Wold, S., 2004: Three-Block Bi-Focal PLS (3BIF-PLS) and its Application in QSAR. SAR and QSAR in Environmental Research 15: 481-499.
Telnarova, M., Vytiskova, S., Chaloupkova, R., Glatz, Z., 2004: Study of Enzymatic Reaction by Electrophoretically Mediated Microanalysis in a Partially Filled Capillary and Indirect or Direct Detection. Electrophoresis 25: 290-296.
Telnarova, M., Vytiskova, S., Monincova, M., Glatz, Z., 2004: Electrophoretically Mediated Microanalysis with Partial Filling Technique and Indirect or Direct Detection as a Tool for Inhibition Studies of Enzymatic Reaction. Electrophoresis 25: 1028-1033.
Stekrova, J., Reiterova, J., Merta, M., Damborsky, J., Zidovska, J., Kebrdlova, V., Kohoutova, M., 2004: PKD2 Mutations in Czech Population with Autosomal Dominant Polycystic Kidney Disease. Nephrology Dialysis Transplantation 19: 1116-1122.
Oakley, A., Klvana, M., Otyepka, M., Nagata, Y., Wilce, M.C.J., Damborsky, J., 2004: Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A Resolution: Dynamics of Catalytic Residues. Biochemistry 43: 870-878.
2003
Prokop, Z., Monincova, M., Chaloupkova, R., Klvana, M., Nagata, Y., Janssen, D.B., Damborsky, J., 2003: Catalytic Mechanism of the Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26. Journal of Biological Chemistry 278: 45094-45100.
Nagata, Y., Prokop, Z., Marvanova, S., Sykorova, J., Monincova, M., Tsuda, M., Damborsky, J., 2003: Reconstruction of Mycobacterial Dehalogenase Rv2579 by Cumulative Mutagenesis of Haloalkane Dehalogenase LinB. Applied and Environmental Microbiology 69: 2349-2355.
Kmunicek, J., Bohac, M., Luengo, S., Gago, F., Wade, R.C., Damborsky, J., 2003: Comparative Binding Energy Analysis of Haloalkane Dehalogenase Substrates: Modelling of Enzyme-Substrate Complexes by Molecular Docking and Quantum Mechanical Calculations. Journal of Computer-Aided Molecular Design 17: 299-311.
Matiasovicova, J., Faldynova, M., Pravcova, M., Karpiskova, R., Kolackova, R., Damborsky, J., Rychlik, I., 2003: Retron Reverse Transcriptase rrtT is Ubiquitous in Strains of Salmonella enterica Serovar Typhimurium. FEMS Microbiology Letters 223: 281-286.
Chaloupkova, R., Sykorova, J., Prokop, Z., Jesenska, A., Monincova, M., Pavlova, M., Tsuda, M., Nagata, Y., Damborsky, J., 2003: Modification of Activity and Specificity of Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26 by Engineering of its Entrance Tunnel. Journal of Biological Chemistry 278: 52622-52628.
Streltsov, V.A., Prokop, Z., Damborsky, J., Nagata, Y., Oakley, A., Wilce, M.C.J., 2003: Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray Crystallographic Studies of Dehalogenation of Brominated Substrates. Biochemistry 42: 10104-10112.
Hatta, T., Mukerjee-Dhar, G., Damborsky, J., Kiyohara, H., Kimbara, K., 2003: Cloning and Characterization of a Novel Thermostable Mn(II)-Dependent 2,3-Dihydroxybiphenyl 1,2-Dioxygenase from a PCB and Naphthalene Degrading Bacillus sp. JF8. Journal of Biological Chemistry 278: 21483-21492.
2002
Rychlik, I., Martin, G., Methner, U., Lovell, M., Cardova, L., Sebkova, A., Sevcik, M., Damborsky, J., Barrow, P.A., 2002: Identification of Salmonella enterica Serovar Typhimurium Genes Associated with Growth Suppression in Stationary-Phase Nutrient Broth Cultures and in the Chicken Intestine. Archives in Microbiology 178: 411-420.
Bohac, M., Loeprecht, B., Damborsky, J., Schuurmann, G., 2002: Impact of Orthogonal Signal Correction (OSC) on the Predictive Ability of CoMFA Models for the Ciliate Toxicity of Nitrobenzenes. Quantitative Structure-Activity Relationships 21: 3-11.
Bohac, M., Nagata, Y., Prokop, Z., Prokop, M., Monincova, M., Tsuda, M., Koca, J., Damborsky, J., 2002: Halide-Stabilizing Residues of Haloalkane Dehalogenases Studied by Quantum Mechanic Calculations and Site-Directed Mutagenesis. Biochemistry 41: 14272-14280.
Jesenska, A., Bartos, M., Czernekova, V., Rychlik, I., Pavlik, I., Damborsky, J., 2002: Cloning, Expression and Preliminary Characterization of Novel Haloalkane Dehalogenase DhmA from Mycobacterium avium N85. Applied and Environmental Microbiology 68: 3724-3730.
Bosma, T., Damborsky, J., Stucki, G., Janssen, D.B., 2002: Biodegradation of 1,2,3-Trichloropropane Through Directed Evolution and Heterologous Expression of a Haloalkane Dehalogenase Gene. Applied and Environmental Microbiology 68: 3582-3587.
Otyepka, M., Damborsky, J., 2002: Functionally Relevant Motions of Haloalkane Dehalogenases Occur in the Specificity-modulating Cap Domains. Protein Science 11: 1206-1217.
Volf, J., Sevcik, M., Havlickova, H., Sisak, F., Damborsky, J., Rychlik, I., 2002: Role of SdiA in Salmonella enterica Serovar Typhimurium Physiology and Virulence. Archives in Microbiology 178: 94-101.
Oakley, A., Prokop, Z., Bohac, M., Kmunicek, J., Jedlicka, T., Monincova, M., Kuta Smatanova, I., Nagata, Y., Damborsky, J., Wilce, M.C.J., 2002: Exploring the Structure and Activity of Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26: Evidence for Product and Water Mediated Inhibition. Biochemistry 41: 4847-4855.
2001
Damborsky, J., Rorije, E., Jesenska, A., Nagata, Y., Klopman, G., Peijnenburg, W.J.G.M., 2001: Structure-Specificity Relationships for Haloalkane Dehalogenases. Environmental Toxicology and Chemistry 20: 2681-2689.
Marvanova, S., Nagata, Y., Wimmerova, M., Sykorova, J., Hynkova, K., Damborsky, J., 2001: Biochemical Characterization of Broad-Specificity Enzymes using Multivariate Experimental Design and A Colorimetric Microplate Assay: Characterization of the Haloalkane Dehalogenase Mutants. Journal of Microbiological Methods 44: 149-157.
Damborsky, J., Prokop, M., Koca, J., 2001: TRITON: graphic software for rational engineering of enzymes. Trends in Biochemical Sciences 26: 71-73.
Machackova, E., Damborsky, J., Valik, D., Foretova, L., 2001: Four Novel Germline BRCA1 and BRCA2 Mutations in Breast and Breast-ovarian Cancer Families from Czech Republic. Human Mutation 18: 545-549.
Zouhar, J., Vevodova, J., Marek, J., Damborsky, J., Su, X.-D., Brzobohaty, B., 2001: Insights into the Functional Architecture of the Catalytic Center of a Maize Beta-Glucosidase Zm-p60.1. Plant Physiology 127: 973-985.
Trantirek, L., Hynkova, K., Nagata, Y., Murzin, A., Ansorgova, A., Sklenar, V., Damborsky, J., 2001: Reaction Mechanism and Stereochemistry of g-hexachlorocyclohexane Dehydrochlorinase LinA. Journal of Biological Chemistry 276: 7734-7740.
Nagata, Y., Mori, K., Takagi, M., Murzin, A.G., Damborsky, J., 2001: Identification of Protein Fold and Catalytic Residues of g-Hexachlorocyclohexane Dehydrochlorinase LinA. Proteins 45: 471-477.
Janda, L., Damborsky, J., Rezniczek, G.A., Wiche, B., 2001: Plectin repeats and modules: strategic cysteines and their presumed impact on cytolinker functions. Bioassays 23: 1064-1069.
Kmunicek, J., Luengo, S., Gago, F., Ortiz, A.R., Wade, R.C., Damborsky, J., 2001: Comparative Binding Energy (COMBINE) Analysis of the Substrate Specificity of Haloalkane Dehalogenase from Xanthobacter autotrophicus GJ10. Biochemistry 40: 8905-8917.
Krejci, L., Damborsky, J., Thomsen, B., Duno, M., Bendixen, Ch., 2001: Molecular Dissection of Interactions between Rad51 and Members of the Recombination-Repair Group. Molecular and Cellular Biology 21: 966-976.
Cajan, M., Damborsky, J., Stibor, I., Koca, J., 2001: Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships. Journal of Chemical Information and Computer Sciences 40: 1151-1157.
2000
Prokop, M., Damborsky, J., Koca, J., 2000: TRITON: In Silico Construction of Protein Mutants and Prediction of their Activities. Bioinformatics 16: 845-846.
Marek, M., Vevodova, J., Kuta Smatanova, I., Nagata, Y., Swensson, L.A., Newman, J., Takagi, M., Damborsky, J., 2000: Crystal Structure of the Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry 39: 14082-14086.
Damborsky, J., Damborska, M., Stipek, S., Jesenska, A., Trantirek, L., Sklenar, V., 2000: Effect of the Carbon Source on Assessment of Degrading Bacteria with the Spread-Plating Technique During In Situ Bioremediation. Folia Microbiologica 45: 35-40.
Glatz, Z., Marini, M.V., Wimmerova, M., Damborsky, J., Nagata, Y., 2000: Determination of Haloalkane Dehalogenase Activity by Capillary Zone Electrophoresis. Journal of Chromatography A 895: 219-225.
Janda, L., Damborsky, J., Petricek, M., Spizek, J., Tichy, P., 2000: Molecular Characterization of the Thermomonospora curvata aglA Gene Encoding a Thermotolerant Alpha-1,4-glucosidase. Journal of Applied Microbiology 88: 773-783.
Jesenska, A., Sedlacek, I., Damborsky, J., 2000: Dehalogenation of Haloalkanes by Mycobacterium tuberculosis H37Rv and Other Mycobacteria. Applied and Environmental Microbiology 66: 219-222.
1999
Damborsky, J., Koca, J., 1999: Analysis of the Reaction Mechanism and Substrate Specificity of Haloalkane Dehalogenases by Sequential and Structural Comparisons. Protein Engineering 12: 989-998.
Damborsky, J., 1999: Tetrachloroethene-dehalogenating Bacteria. Folia Microbiologica 44: 247-262.
Nagata, Y., Hynkova, K., Damborsky, J., Takagi, M., 1999: Construction and Characterization of Histidine-tagged Haloalkane Dehalogenase (LinB) of a New Substrate Class from a gamma-hexachlorocyclohexane-degrading Bacterium, Sphingomonas paucimobilis UT26. Protein Expression and Purification 17: 229-304.
Damborsky, J., Damborska, M., Pistek, V., 1999: Sporulation as an Effective Strategy for the Survival of Bacteria in a Biofilter with Discontinuous Operation. Biotechnology Letters 21: 835-838.
Hynkova, K., Nagata, Y., Takagi, M., Damborsky, J., 1999: Identification of the Catalytic Triad in the Haloalkane Dehalogenase from Sphingomonas paucimobilis UT25. FEBS Letters 446: 177-181.
1998
Lynam, M., Kuty, M., Damborsky, J., Koca, J. and Adriaens, P., 1998: Molecular Orbital Calculations to Describe Microbial Reductive Dechlorination of Polychlorinated Dioxins. Environmental Toxicology and Chemistry 17: 988-997.
Blaha, L., Damborsky, J., and Nemec, M., 1998: QSAR for Acute Toxicity of Saturated and Unsaturated Halogenated Compounds. Chemosphere 36: 1345-1365.
Damborsky, J., Bohac, M., Prokop, M., Kuty, M., Koca, J., 1998: Computational Site-directed Mutagenesis of Haloalkane Dehalogenase in Position 172. Protein Engineering 11: 901-907.
Damborsky, J., Berglund, A., Kuty, M., Ansorgova, A., Nagata, Y., Sjoestroem, M., 1998: Mechanism-Based Structure-Biodegradability Relationships for Hydrolytic Dehalogenation of Chloro- and Bromo- Alkenes. Quantitative Structure-Activity Relationships 17: 450-458.
Damborsky, J., 1998: Computer Modelling of Microbial Hydrolytic Dehalogenation. Pure & Applied Chemistry 70: 1375-1383.
Kuty, M., Damborsky, J., Prokop, M. and Koca, J., 1998: A Molecular Modelling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 2. Quantum Chemical Study of Complete Reaction Mechanism. Journal of Chemical Information and Computer Sciences 38: 736-741.
Damborsky, J., 1998: Quantitative Structure-Function and Structure-Stability Relationships of Purposely Modified Proteins. Protein Engineering 11: 21-30.
1997
Damborsky, J., Kuty, M., Nemec, M. and Koca, J., 1997: A Molecular Modelling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 1. Quantum Chemical Study of the First Reaction Step. Journal of Chemical Information and Computer Sciences 37: 562-568.
Damborsky, J., Nyandoroh, M., Nemec, M., Holoubek, I., Bull, A. and Hardman, D., 1997: Some Biochemical Properties and the Classification of a Range of Bacterial Haloalkane Dehalogenases. Biotechnology and Applied Biochemistry 26: 19-25.
Damborsky, J., 1997: Quantitative Structure-Function Relationships of the Single-point Mutants of Haloalkane Dehalogenase: A Multivariate Approach. Quantitative Structure-Activity Relationships 16: 1-10.
Damborsky, J., Manova, K., Berglund, A., Sjostrom, M. and Nemec, M., 1997: Biotransformation of Chloro- and Bromoalkenes by Crude Extracts of Rhodococcus erythropolis Y2. Advances in Environmental Research 1: 50-57.
Damborsky, J. and Schultz, T., 1997: Comparison of the QSAR Models for Toxicity and Biodegradability of Anilines and Phenols. Chemosphere 34: 429-446.
Krooshof, G.H., Kwant, E.M., Damborsky, J., Koca, J., Janssen, D.B., 1997: Repositioning the Catalytic Triad Aspartic Acid of Haloalkane Dehalogenase: Effects on Stability, Kinetics and Structure. Biochemistry 36: 9571-9580.
Nagata, Y., Miyauchi, K., Damborsky, J., Manova, K., Ansorgova, A. and Takagi, M., 1997: Purification and Characterization of Haloalkane Dehalogenase of a New Substrate Class from a g-Hexachlorocyclohexane-Degrading Bacterium, Sphingomonas paucimobilis UT26. Applied and Environmental Microbiology 63: 3707-3710.
1996
Damborsky, J., 1996: A Mechanistic Approach to Deriving Quantitative Structure-Activity Relationship Models for Microbial Degradation of Organic Compounds. SAR and QSAR in Environmental Research 5: 27-36.
1995
Damborsky, J., Bull, A. and Hardman, D., 1995: Homology Modelling of the Haloalkane Dehalogenase of Sphingomonas paucimobilis UT26. Biologia 50: 523-528.
Hermens, J., Balaz, S., Damborsky, J., Karcher, W., Muller, M., Peijnenburg, W., Sabljic, A. and Sjostrom, M., 1995: Assessment of QSARs for Predicting Fate and Effects of Chemicals in the Environment: An International European Project. SAR and QSAR in Environmental Research 3: 223-236.
1991
Smarda, J., Damborsky, J., 1991: A Quantitative Assay of Group E Colicins. Scripta Medica 64: 111-118.
Book chapters
Vilim, J., Prokop, Z., Damborsky, J., 2023: Software Tools for Optimization of Biocatalysts. In: Greetal, C., Prashanth, R., Comprehensive Chirality, 2nd edition, Elsevier, pp. xxx.
Uhrik, L., Henek, T., Planas-Iglesias, J., Kucera, J., Damborsky, J., Marek, M., Hernychova, L., 2023: Study of Protein Conformational Dynamics Using Hydrogen/Deuterium Exchange Mass Spectrometry. In: Sousa, Â., Passarinha, L. (Eds.), Advanced Methods in Structural Biology, Methods in Molecular Biology 2652, Humana, New York, pp. 293-318.
Sykora, J., Prokop, Z., Damborsky, J., Abhinav, Hof, M., Amaro, M., 2023: Dynamics and Hydration of Proteins Viewed by Fluorescence Methods: Investigations for Protein Engineering and Synthetic Biology. In: Šachl, R., Amaro, M. (Eds.), Fluorescence Spectroscopy and Microscopy in Biology, Springer, Cham, pp. 509–532.
Hozzova, J., Vavra, O., Bednar, D., Filipovic, J., 2021: Simulation of Ligand Transport in Receptors Using CaverDock. In: Ballante F. (Ed.), Protein-Ligand Interactions and Drug Design, Methods in Molecular Biology, Humana, New York, pp. 105-124.
Vasina, M., Vanacek, P., Damborsky, J., Prokop, Z., 2020: Exploration of Enzyme Diversity: High-Throughput Techniques for Protein Production and Microscale Biochemical Characterization. In: Dan S. Tawfik (Ed.), Methods in Enzymology, Academic Press, pp. 51-85.
Prokop, Z., Gross, J., Hall, M., 2020: Access to (S)-4-Bromobutan-2-ol through Selective Dehalogenation of rac-1, 3-Dibromobutane by Haloalkane Dehalogenase. In: Whittall, J., Sutton, P. W. (Eds.), Applied Biocatalysis: The Chemist's Enzyme Toolbox, John Wiley & Sons, Ltd., pp. 354-359.
Prokop, Z., Bidmanova, S., Koudelakova, T., Damborsky, J., 2018: Enzymes for Detection and Decontamination of Chemical Warfare Agents. In: Williams, G., Hall, M. (Eds.), Modern Biocatalysis: Advances Towards Synthetic Biological Systems, Royal Society of Chemistry, Cambridge, pp. 539-565.
Mazurenko, S., Damborsky, J., Prokop, Z., 2017: Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets. In: Fdez-Riverola, F., Mohamad, M. S., Rocha, M., De Paz, J. F., Pinto, T., Advances in Intelligent Systems and Computing 616, Springer, New York, pp. 9-17.
Brezovsky, J., Kozlikova, B., Damborsky, J., 2017: Computational Analysis of Protein Tunnels and Channels. In: Bornscheuer, U. T., Höhne, M. (Eds.), Protein Engineering. Methods and Protocols, Springer, New York, pp. 25-42.
Kokkonen, P., Koudelakova, T., Chaloupkova, R., Daniel, L., Prokop, Z., Damborsky, J., 2017: Structure-function Relationships and Engineering of Haloalkane Dehalogenases. In: Rojo, F., Handbook of Hydrocarbon and Lipid Microbiology Series. Aerobic Utilization of Hydrocarbons, Oils, and Lipids, Springer, Heidelberg, pp. 1-21.
Marques, S. M., 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.
Stepankova, V., Damborsky, J., Chaloupkova, R., 2015: Hydrolases in Non-Conventional Media: Implications for Industrial Biocatalysis. In: Peter Grunwald, Industrial Biocatalysis, Pan Stanford Publishing, pp. 583-620.
Sebestova, E., Bendl, J., Brezovsky, J., Damborsky, J., 2014: Computational Tools for Designing Smart Libraries. In: Gillam, E. M. J., Copp, J. N., Ackerley, D. F., (Eds.), Directed Evolution Library Creation: Methods and Protocols, Methods in Molecular Biology, 2nd edition, Humana Press, New York, pp. 291-314.
Bidmanova, S., Hrdlickova, E., Koudelakova, T., Damborsky, J., Prokop, Z., 2013: On-line Monitoring of Biodegradation Processes using Enzymatic Biosensors. In: Nojiri, H., Tsuda, M., Fukuda, M., Kamagata, Y., (Eds.), Biodegradative Bacteria, Springer, Japan, pp. 155-180.
Prokop, Z., Stepankova, V., Hasan, K., Chaloupkova, R., Damborsky, J., 2012: Preparation of Optically Pure Haloalkanes and Alcohols by Kinetic Resolution using Haloalkane Dehalogenases. In: John Whittall and Peter Sutton (Eds.), Practical Methods for Biocatalysis and Biotransformations, 2nd ed., John Wiley & Sons, Chichester, pp. 307-313.
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.
Jesenska, A., Damborsky, J., 2009: Degradation of Organic Compounds by Mycobacteria. In: Kazda, J., Pavlik, I., Falkinham III, J.O., Hruska, K. (Eds.), The Ecology of Mycobacteria: Impact on Animal's and Human's Health, Springer, Berlin, pp. 314-329.
Damborsky, J., Chaloupkova, R., Pavlova, M., Chovancova, E., Brezovsky, J., 2009: Structure-Function Relationships and Engineering of Haloalkane Dehalogenases. In: Kenneth N. Timmis (Ed.), Handbook of Hydrocarbon and Lipid Microbiology, Springer, Berlin, Heidelberg, pp. 1081-1098.
Damborsky, J., Kmunicek, J., Jedlicka, T., Luengo, S., Gago, F., Ortiz, A.R., Wade, R.C., 2003: Rational Re-design of Haloalkane Dehalogenases Guided by Comparative Binding Energy Analysis. In: Svendsen, A. (Ed.), Enzyme Functionality: Design, Engineering and Screening, Marcel Decker, New York, pp. 79-96.
Janssen, D.B., Damborsky, J., Rink, R., Krooshof, G., 2000: Engineering Proteins for the Biodegradation of Recalcitrant Compounds. In: L. Alberghina (Ed.), Protein Engineering in Industrial Biotechnology, Harwood Academic Publishers, Amsterdam, pp. 227-244.
Damborsky, J., Lynam, M., and Kuty, M., 1998: Structure- Biodegradability Relationships for Chlorinated Dinbenzo-p-Dioxins and Dibenzofurans. In: R.-M. Wittich (Ed.), Biodegradation of Dioxins and Furans, R.G. Landes, Austin, pp. 165-228.
Damborsky, J., Kuty, M., Nemec, M. and Koca, J., 1997: Molecular Modelling to Understand the Mechanisms of Microbial Degradation – Application to Hydrolytic Dehalogenation with Haloalkane Dehalogenases. In: F. Chen and G. Schuurmann (Eds.), Quantitative Structure-Activity Relationships in Environmnetal Sciences - VII, SETAC Press, Pensacola, pp. 5-20.
Peijnenburg, W.J.G.M., Damborsky, J., 1996: Introduction, Main Conclusions and Recommendations of the Workshop `QSAR Biodegradation II’. In: Peijnenburg, W.J.G.M., Damborsky, J., Eds., Biodegradability Prediction, Kluwer Academic Publishers, Dordrecht, pp. 143.
Adriaens, P., Barkovskii, A.L., Lynam, M., Damborsky, J. and Kuty, M., 1996: Polychlorinated Dibenzo-p-Dioxins in Anaerobic Soils and Sediments. In: W.J.G.M. Peijnenburg and J. Damborsky (Eds.), Biodegradability Prediction, Kluwer Academic Publishers, Dordrecht, pp. 51-64.
Damborsky, J., Manova, K. and Kuty, M., 1996: A Mechanistic Approach to Deriving Quantitative Structure-Biodegradability Relationships. A Case Study: Dehalogenation of Haloaliphatic Compounds. In: W.J.G.M. Peijnenburg and J. Damborsky (Eds.), Biodegradability Prediction, Kluwer Academic Publishers, Dordrecht, pp. 75-92.
Patents
Paruch, K., Carbain, B., Havel, S., Damborský, J., Brezovský , J., Daniel, L.; Sisáková, A.; Nikulenkov, F., Krejčí, L., 2023: Substituted Aminothiazoles as Inhibitors of Nucleases. Masaryk University, Brno, Czech Republic. Patent US 11,584,742 B2.
Toul, M., Smith, A., Marek, M., Pinto, J. G., Planas-Iglesias, J., Pluskal, D., Vasina, M., Bednar, D., Prokop, Z., Damborsky, J., 2023: Coelenterazine-Utilizing Luciferases with Stable Glow-Type Light Emission, Increased Substrate Affinity, Suppresed Product Inhibition, and Modulated Emission Wavelengths, and Methods of Producing and Using Thereof. Masaryk University, Brno, Czech Republic. Patent WO/2023/021023.
Dvorak, P., Krejci, P., Balek, L., Eiselleova, L., Konecna, Z., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Stepankova, V., Vanacek, P., Prokop, Z., Damborsky, J., Bosakova, M., 2023: Thermostable FGF2 Polypeptide, Use Thereof. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent US 11,746,135 B2.
Paruch, K., Carbain, B., Havel, S., Damborský, J., Brezovský , J., Daniel, L.; Sisáková, A.; Nikulenkov, F., Krejčí, L., 2023: Substituted Aminothiazoles as Inhibitors of Nucleases. Masaryk University. Patent IL277866.
Dvorak, P., Krejci, P., Balek, L., Eiselleova, L., Konecna, Z., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Stepankova, V., Vanacek, P., Prokop, Z., Damborsky, J., Bosakova, M., 2023: Thermostable FGF2 Polypeptide, Use Thereof. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent IN485239.
Dvorak, P., Krejci, P., Balek, L., Eiselleova, L., Konecna, Z., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Stepankova, V., Vanacek, P., Prokop, Z., Damborsky, J., Bosakova, M., 2022: Thermostable FGF2 Polypeptide, Use Thereof. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent JP7131772.
Dvorak, P., Krejci, P., Balek, L., Eiselleova, L., Konecna, Z., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Stepankova, V., Vanacek, P., Prokop, Z., Damborsky, J., Bosakova, M., 2021: Thermostable FGF2 Polypeptide. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent SG 11201804402W.
Chaloupkova, R., Stepankova, V., Petulova, E., Ghazalova, T., Damborsky, J., Bednar, D., 2021: Termostabilní polypeptid na bázi FGF18 a jeho použití. St. Anne's University Hospital Brno and Enantis, s.r.o., Brno, Czech Republic. Patent XX.
Damborsky, J., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Balek, L., Krejci, P., Dvorak, P., Konecna, Z., Eiselleova, L., Bosakova, M., Vanacek, P., Stepankova, V., Prokop, Z., 2020: Thermostable FGF2 Polypeptide, Use thereof and Culture Medium Containing Thermostable FGF2 Polypeptide. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent EP3380508B1.
Bidmanova, S., Prokop, Z., Damborsky, J., Durkop, A., Wolfbeis, O. S., 2019: Device for Detection of Halogenated Hydrocarbons. Masaryk University, Brno, Czech Republic. Patent EP 3173487B1.
Paruch, K., Carbain, B., Havel, S., Damborsky, J., Brezovsky, J., Daniel, L., Sisakova, A., Nikulenkov, F., Krejci, L., 2017: Pyrazolotriazines as Inhibitors of Nucleases. Masaryk University, Brno, Czech Republic. Patent EP 2957562.
Damborsky, J., Nikulenkov, F., Sisakova, A., Havel, S., Krejci, L., Carbain, B., Brezovsky, J., Daniel, L., Paruch, K., 2015: Pyrazolotriazines as Inhibitors of Nucleases. Masaryk University, Brno, Czech Republic. Patent WO 2015/192817 A1.
Damborsky, J., Prokop, Z., Koudelakova, T., Stepankova, V., Chaloupkova, R., Gora, A., Chovancova, E., Brezovsky, J., 2013: Method of Thermostabilization of a Protein and/or Stabilization Towards Organic Solvents. Masaryk University, Brno, Czech Republic. Patent US 8,580,932.
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