Publications

2017

Buryska, T., Babkova, P., Vavra, O., Damborsky, J., Prokop, Z., 2017: A Haloalkane Dehalogenase From a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity. Applied and Environmental Microbiology XX: XXX-XXX.

Mazurenko, S., Kunka, A., Beerens, K., Damborsky, J., Prokop, Z., 2017: Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating. Scientific Reports XX: XXX-XXX.

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 6: 349–360.

Mazurenko, S., Damborsky, J., Prokop, Z., 2017: Multi-enzyme pathway optimisation through star-shaped reachable sets. Advances in Intelligent Systems and Computing 616: 9-17.

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(3): XXX-XXX.

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.

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.

Marques, S. M., Daniel, L., Buryska, T., Prokop, Z., Brezovsky, J., Damborsky, J., 2016: Enzyme Tunnels and Gates as Relevant Targets in Drug Design. Medicinal Research Reviews 37: 1095-1139.

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., Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Grüning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M.C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J.W., Licata, L., Mareuil, F., Mičetić, I., Friborg, R.M., Moretti, S., Morris, C., Möller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwämmle, V., Smith, C., Sperotto, M.M., Stockinger, H., Svobodová Vařeková, R., Tosatto, S.C., de la Torre V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Løngreen, P., Brunak, S., 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

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.

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.

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: Mycobacterial Haloalkane Dehalogenases: Cloning, Biochemical Properties and Distribution. 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., 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.

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.

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.

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.

2003

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.

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.

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.

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.

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.

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.

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.

2002

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.

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.

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.

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.

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.

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.

Otyepka, M., Damborsky, J., 2002: Functionally Relevant Motions of Haloalkane Dehalogenases Occur in the Specificity-modulating Cap Domains. Protein Science 11: 1206-1217.

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

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.

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.

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.

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., 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.

Damborsky, J., Prokop, M., Koca, J., 2001: TRITON: graphic software for rational engineering of enzymes. Trends in Biochemical Sciences 26: 71-73.

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.

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.

Damborsky, J., 1998: Quantitative Structure-Function and Structure-Stability Relationships of Purposely Modified Proteins. Protein Engineering 11: 21-30.

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.

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

Brezovsky, J., Kozlikova, B., Damborsky, J., 2018: 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

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., 2015: Thermostable FGF2 Polypeptide, Use thereof and Culture Medium Containing Thermostable FGF2 Polypeptide. Masaryk University and Enantis, s.r.o., Brno, Czech Republic. Patent application EP 15196802.1.

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.

Bidmanova, S., Prokop, Z., Damborsky, J., Dürkop, A., Wolfbeis, O.S., 2015: Device for Detection of Halogenated Hydrocarbons. Masaryk University, Brno, Czech Republic. Patent application number EP 15196591.

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.

Prokop, Z., Damborsky, J., Oplustil, F., Jesenska, A., Nagata, Y., 2005: Method of Detoxification of Yperite by using Haloalkane Dehalogenases. Masaryk University, Brno, Czech Republic. Patent WO 2006/128390 A1.

Prokop, Z., Damborsky, J., Nagata, Y., Janssen, D.B., 2004: Method of Production of Optically Active Hydrocarbons and Alcohols Using Hydrolytic Dehalogenation Catalysed by Haloalkane Dehalogenases. Masaryk University, Brno, Czech Republic. Patent WO 2006/079295 A2.

Ondrej Vavra celebrating success with his presentation on CaverDock
Lecture by Dr. Stavrakis from ETH Zurich
High evaluation of the team’s research performance
Klaudia Chmelova and Veronika Liskova passed doctoral state exam
ELIXIR CZ annual conference 15 – 16 Nov, 2017
New video explaining the goals of Rafts4Biotech EU project
Invitation to a presentation by Synthetic Genomics