Publications


YearJournal

2016

Pavelka, A., Šebestová, E., Kozlíková, B., Brezovský, J., Sochor, J., Damborský, J.: CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13(3), 2016.

2014

Kozlíková, B., Šebestová, E., Šustr, V., Brezovský, J., Strnad, O., Daniel, L., Bednář, D., Pavelka, A., Maňák, M., Bezděka, M., Beneš, P., Kotry, M., Gora, A. W., Damborský, J., Sochor, J.: CAVER Analyst 1.0: Graphic Tool for Interactive Visualization and Analysis of Tunnels and Channels in Protein Structures, Bioinformatics, 30(18), 2014.

2013

Gora, A., Brezovský, J., Damborský, J.: Gates of Enzymes, Chemical Reviews, 113, 5871–5923, 2013.
Brezovský, J., Chovancová, E., Gora, Pavelka, A., Biedermannová, L., Damborský, J.: Software Tools for Identification, Visualization and Analysis of Protein Tunnels and Channels, Biotechnology Advances , 31, 38-49, 2013.
Damborský, J., Prokop, Z., Koudeláková, T., Štěpánková, V., Chaloupková, R., Gora, A., Chovancová, E., Brezovský, J.: Method of Thermostabilization of a Protein and/or Stabilization Towards Organic Solvents, Masaryk University, Brno, Czech Republic. Patent US 8,580,932, 2013.
CaverSoft: CAVER Analyst - Engineering Enzymes by Modification Of Access Tunnels, poster at Biotrans, 2013.

2012

Chovancová,E., Pavelka, A., Beneš, P., Strnad, O., Brezovský, J., Kozlíková, B., Gora, A., Šustr, V., Klvaňa, M., Medek, P., Biedermannová, L., Sochor, J., Damborský, J.: CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures, PLoS Computational Biology 8: e1002708, 8(10), 2012.

2011

Chovancová E., Pavelka A., Beneš P., Strnad O., Brezovský J., Kozlíková B., Gora A., Šustr V., Klvaňa M., Medek P., Biedermannová L., Damborský J., Sochor J.: CAVER 3.0, software, 2011.

2010

Kozlíková B., Sochor J., Szabó T., Zamborský M.: CAVER Viewer - new tool enhancing computation and visualization of channels in proteins, IADIS Computer Graphics, Visualization, Computer Vision and Image Processing (CGVCVIP), 2010, ISBN 978-972-8939-22-9.
Beneš P., Medek P., Sochor J.: Tracking single channel in protein dynamics, WSCG Communication Papers proceedings, 109-114, 2010, ISBN 978-80-86943-87-9.
Beneš P., Chovancová E., Kozlíková B., Pavelka A., Strnad O., Brezovský J., Šustr V., Klvaňa M., Szabó T., Gora A., Zamborský M., Biedermannová L., Medek P., Damborský J., Sochor J.: CAVER 2.1, software, 2010.

2009

Beneš P., Medek P., Sochor J.: Computation of channels in protein dynamics, Proceedings of the IADIS International Conference Applied Computing 2009, IADIS Press Rome, 251-258, 2009, ISBN 978-972-8924-97-3.
Klvaňa, M., Pavlová, M., Koudeláková, T., Chaloupková, R., Dvořák, P., Prokop, Z., Stsiapanava, A., Kutý, M., Kutá-Smatanová, I., Dohnálek, J., Kulhánek, P., Wade, R.C., Damborský, J.: 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, 2009.
Pavlová, M., Klvaňa, M., Chaloupková, R., Banáš, P., Otyepka, M., Wade, R., Nagata, Y., Damborský, J.: Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate, Nature Chemical Biology, 5, 727-733, 2009.

2008

Medek P., Beneš P., Sochor J.: Multicriteria Tunnel Computation, CGIM '08 Proceedings of the Tenth IASTED International Conference on Computer Graphics and Imaging, Insbruck, Austria, 160-164, 2008, ISBN 978-0-88986-720-8.
Medek P., Beneš P., Sochor J.: Computation of more channels in protein molecules, Proceedings Conference Visual Computing For Biomedicine (VCBM), Aire-la-Ville, Switzerland, 45-51, 2008, ISBN 978-3-905674-13-2.
Medek P., Beneš P., Kozlíková B., Chovancová E., Pavelka A., Szabó T., Zamborský M., Andres F., Klvaňa M., Brezovský J., Sochor J., Damborský J.: CAVER 2.0, software, 2008.

2007

Kozlíková B., Andres F., Sochor J.: Visualisation of Tunnels in Protein Molecules, AFRIGRAPH '07 Proceedings of the 5th international conference on Computer graphics, virtual reality, visualisation and interaction in Africa, 111-118, 2007, ISBN 978-1-59593-906-7.
Damborský J., Petřek M., Banáš P., Otyepka M.: Identification of Tunnels in Proteins, Nucleic Acids, Inorganic Materials and Molecular Ensembles, Biotechnology Journal, 2, 62-67, 2007.
Medek, P., Beneš, P., Sochor, J.: Computation of tunnels in protein molecules using Delaunay triangulation, Journal of WSCG, 15(1-3), 107-114, 2007, 978-80-86943-00-8.

2006

Petřek, M., Otyepka, M., Banáš, P., Košinová, P., Koča, J., Damborský, J.: CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities, BMC Bioinformatics, 7, 316, 2006.

YearJournal

2016

Marques, S. M., Daniel, L., Buryška, T., Prokop, Z., Brezovský, J., Damborský, J.: Enzyme Tunnels and Gates as Relevant Targets in Drug Design, Medicinal Research Reviews, in press, 2016.
Kaushik, S., Prokop, Z., Damborský, J., Chaloupková, R.: Kinetics of Binding of Fluorescent Ligands to Enzymes with Engineered Access Tunnels, FEBS Journal, in press, 2016.
Brezovský, J., Babková, P., Degtjarik, O., Fořtová, A., Gora, A., Iermak, I., Řezáčová, P., Dvořák, P., Kutá Smatanová, I., Prokop, Z., Chaloupková, R., Damborský, J.: Engineering a de Novo Transport Tunnel, ACS Catalysis, 6, 7597-7610, 2016.
Bendl, J., Šťourač, J., Šebestová, E., Vávra, O., Musil, M., Brezovský, J., Damborský, J.: HotSpot Wizard 2: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering, Nucleic Acids Research, 44, W479-W487, 2016.

2015

Lišková, V., Bednář, D., Holubeva, T., Prudniková, T., Řezáčová, P., Koudeláková, T., Šebestová, E., Kutá Smatanová, I., Brezovský, J., Chaloupková, R., Damborský, J.: Balancing the Stability-Activity Trade-off by Fine-Tuning Dehalogenase Access Tunnels, ChemCatChem, 7(4), 648–659, 2015.

2014

Sýkora, J., Brezovský, J., Koudeláková, T., Lahoda, M., Fořtová, A., Chernovets, T., Chaloupková, R., Štěpánková, Prokop, Z., Kutá Smatanová, I., Hof, M., Damborský, J.: Dynamics and Hydration Explain Failed Functional Transformation in Dehalogenase Design, Nature Chemical Biology, 10, 428–430, 2014.
Damborský, J., Brezovský, J.: Computational tools for designing and engineering enzymes, Current Opinion in Chemical Biology, 19, 8-16, 2014.

2013

Lahoda, M., Stsiapanava, A., Chaloupková, R., Mesters, J.R., Damborský, J., Kutá Smatanová, I.: Crystallographic Analysis of 1,2,3–Trichloropropane Biodegradation by Haloalkane Dehalogenase DhaA31, Acta Crystallographica D, 70, 209-217, 2013.
Amaro, M., Brezovský, J., Kováčová, S., Maier, L., Chaloupková, R., Sýkora, J., Paruch, K., Damborský, J., Hof, M.: Are Time-Dependent Stokes Shifts at the Tunnel Mouth of Haloalkane Dehalogenase Enzymes Dependent on the Choice of the Chromophore?, Journal of Physical Chemistry, 117, 7898-7906, 2013.
Štěpánková, V., Khabiri, M., Brezovský, J., Pavelka, A., Minofar, B., Prokop, Z., Ettrich, R., Chaloupková, R., Damborský, J.: Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Co-solvents, ChemBioChem, 14, 890-897, 2013.
Štěpánková, V., Damborský, J., Chaloupková, R.: Organic co-solvents affect activity, stability and enantioselectivity of haloalkane dehalogenases, Biotechnology Journal , 8, 719-729, 2013.
Štěpánková, V., Paterová, J., Damborský, J., Jungwirth, P., Chaloupková, R., Heyda, J.: Cation Specific Effects on Enzymatic Catalysis Driven by Interactions at the Tunnel Mouth of Haloalkane Dehalogenase, Journal of Physical Chemistry B, 117, 6394-6402, 2013.
Koudeláková, T., Chaloupková, R., Brezovský, J., Prokop, Z., Pavlová, M., Hessler, M., Khabiri, M., Ettrich, R., Bornscheuer, U.T., Damborský, J.: Engineering Protein Resistance to Organic Co-solvent and Elevated Temperature by Access Tunnel Modification, Angewandte Chemie International Edition , 52, 1959-1963, 2013.
Davids, T., Schmidt, M., Böttcher, D., Bornscheuer, U.T.: Strategies for the discovery and engineering of enzymes for biocatalysis, Current Opinion in Chemical Biology, 17, 215–220, 2013.

2012

Biedermannová, L., Prokop, Z., Gora, A., Kovács, M., Damborský, J., Wade, R.C.: A Single Mutation in the Access Tunnel Changes Mechanism of Product Release in Haloalkane Dehalogenase LinB, . Journal of Biological Chemistry , 287, 29062-29074, 2012.

2011

Lahoda, M., Chaloupková, R., Stsiapanava, A., Damborský, J., Kutá Smatanová, I.: Crystallization and Crystallographic Analysis of the Rhodococcus rhodochrous NCIMB 13064 Mutant DhaA31 and its Complex with 1,2,3-Trichloropropane, Acta Crystallographica , 67, 397-400, 2011.

2010

Prokop, Z., Sato, Y., Brezovský, J., Mozga, T., Chaloupková, R., Koudeláková, T., Jeřábek, P., Štěpánková, V., Natsume, R., van Leeuwen, J.G.E., Janssen, D.B., Florián, J., Nagata, Y., Senda, T., Damborský, J.: Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering, Angewandte Chemie , 49, 6111-6115, 2010.
Stsiapanava, A., Dohnálek, J., Gavira, J.A., Kutý, M., Koudeláková, T., Damborský, J., Kutá Smatanová, I.: Atomic Resolution Studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels, Acta Crystallographica D, 66, 962-969, 2010.

2009

Pavelka, A., Chovancová, E., Damborský, J.: HotSpot Wizard: A Web Server for Identification of Hot Spots in Protein Engineering, Nucleic Acids Research , 37, W376–W383, 2009.
Damborský, J., Brezovský, J.: Computational Tools for Designing and Engineering Biocatalysts, Current Opinion in Chemical Biology , 13, 26-34, 2009.
Jesenská, A., Sýkora, J., Olżyńska, A., Brezovský, J., Zdráhal, Z., Damborský, J., Hof, M.: Nanosecond Time-Dependent Stokes Shift at the Tunnel Mouth of Haloalkane Dehalogenases, Journal of the American Chemical Society , 131, 494-501, 2009.

2007

Negri, A., Marco, E., Damborský, J., Gago, F.: 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, 2007.
Recommended citations:
CAVER Analyst Kozlíková, B., Šebestová, E., Šustr, V., Brezovský, J., Strnad, O., Daniel, L., Bednář, D., Pavelka, A., Maňák, M., Bezděka, M., Beneš, P., Kotry, M., Gora, A. W., Damborský, J., Sochor, J.: CAVER Analyst 1.0: Graphic Tool for Interactive Visualization and Analysis of Tunnels and Channels in Protein Structures, Bioinformatics, 30(18), 2014.
[BibTeX]
CAVER, CAVER Plugin Chovancová,E., Pavelka, A., Beneš, P., Strnad, O., Brezovský, J., Kozlíková, B., Gora, A., Šustr, V., Klvaňa, M., Medek, P., Biedermannová, L., Sochor, J., Damborský, J.: CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures, PLoS Computational Biology 8: e1002708, 8(10), 2012.
[BibTeX]
CAVER, CAVER Plugin Pavelka, A., Šebestová, E., Kozlíková, B., Brezovský, J., Sochor, J., Damborský, J.: CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13(3), 2016.
[BibTeX]



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