CAVER - software tool for protein analysis and visualization

Publications

Publications describing CAVER Publications employing CAVER

Year	Journal

2018

Brezovský J., Kozlíková B., Damborský J.: Computational Analysis of Protein Tunnels and Channels, Protein Engineering: Methods and Protocols, Methods in Molecular Biology, Uwe T. Bornscheuer and Matthias Hohne (eds.),, vol. 1685, pp 25-42, 2018, 978-1-4939-7364-4.

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. : CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories., Bioinformatics, bty386, 2018.

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.

Year	Journal

2022

Lea R. Rapp, Sérgio M. Marques, Bernd Nebel, Jiri Damborsky, Bernhard Hauer: Engineering CYP153AM.aq to Oxyfunctionalize its Inhibitor Dodecylamine Using a LC/MS Based Rapid Flow Analysis Screening, ChemCatChem, 14, 2022.

Sérgio M. Marques, Michaela Slanska, Klaudia Chmelova, Radka Chaloupkova, Martin Marek, Spencer Clark, Jiri Damborsky, Eric T. Kool, David Bednar, and Zbynek Prokop: Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling, JACS Au, 2(6), 1324-1337, 2022.

Prakinee, Kridsadakorn, Aisaraphon Phintha, Surawit Visitsatthawong, Narin Lawan, Jeerus Sucharitakul, Chadaporn Kantiwiriyawanitch, Jiri Damborsky, Penchit Chitnumsub, Karl-Heinz Van Pee, and Pimchai Chaiyen: Mechanism-guided tunnel engineering to increase the efficiency of a flavin-dependent halogenase, Nature Catalysis, 5.6, 534-544, 2022.

Vavra, Ondrej, Jiri Damborsky, and David Bednar: Fast approximative methods for study of ligand transport and rational design of improved enzymes for biotechnologies, Biotechnology Advances, 108009, 2022.

2021

Schenkmayerova, A., Pinto, G.P., Toul, M., Marek, M., Hernychova, L., Planas-Iglesias, J., Daniel Liskova, V., Pluskal, D., Vasina, M., Emond, S. and Dörr, M.: Engineering the protein dynamics of an ancestral luciferase, Nature Communications, 12, 3616, 2021.

Iermak, I., Degtjarik, O., Havlickova, P., Kuty, M., Chaloupkova, R., Damborsky, J., Prudnikova, T. and Kuta Smatanova, I.: Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum, Catalysts, 11(1), 2021.

Marques, S.M., Planas-Iglesias, J. and Damborsky, J.: Web-based tools for computational enzyme design, Current Opinion in Structural Biology, 69, 19-34, 2021.

Pinto, Gaspar P., Ondrej Vavra, Sergio M. Marques, Jiri Filipovic, David Bednar, and Jiri Damborsky: 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, 2021.

Rapp, Lea R., Sérgio M. Marques, Erna Zukic, Benjamin Rowlinson, Mahima Sharma, Gideon Grogan, Jiri Damborsky, and Bernhard Hauer: Substrate Anchoring and Flexibility Reduction in CYP153AM.aq Leads to Highly Improved Efficiency toward Octanoic Acid, ACS Catalysis, 11, no. 5, 3182-3189, 2021.

2020

Furmanová, Katarína, Ondřej Vávra, Barbora Kozlíková, Jiří Damborský, Vojtěch Vonásek, David Bednář, and Jan Byška: DockVis: Visual Analysis of Molecular Docking Trajectories, Computer Graphics Forum, 36,6, 452-464, 2020.

2019

Stourac, Jan, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar Pinto, Jan Brezovsky, Jiri Damborsky, and David Bednar: Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport, Nucleic acids research, 47, W414-W422, 2019.

Byška, J., Trautner, T., Marques, S.M., Damborský, J., Kozlíková, B. and Waldner, M.: Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization, Computer Graphics Forum, Vol. 38, No. 3, 441-453, 2019.

Pinto, G.P., Vavra, O., Filipovic, J., Stourac, J., Bednar, D. and Damborsky, J.: Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock, Frontiers in Chemistry, 7, 709, 2019.

Vavra, O., Filipovic, J., Plhak, J., Bednar, D., Marques, S.M., Brezovsky, J., Stourac, J., Matyska, L. and Damborsky, J.: CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels , Bioinformatics, , 35(23), 4986-4993, 2019.

Filipovič, J., Vávra, O., Plhák, J., Bednář, D., Marques, S.M., Brezovský, J., Matyska, L. and Damborský, J.: CaverDock: A Novel Method for the Fast Analysis of Ligand Transport, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(5), 1625-1638, 2019.

Kokkonen, P., Bednar, D., Pinto, G., Prokop, Z. and Damborsky, J.: Engineering enzyme access tunnels, Biotechnology advances, 37(6), 107386, 2019.

Marques, S.M., Bednar, D. and Damborsky, J.: Computational Study of Protein-Ligand Unbinding for Enzyme Engineering, Frontiers in chemistry, 6, 650, 2019.

2018

Vanacek, P., Sebestova, E., Babkova, P., Bidmanova, S., Daniel, L., Dvorak, P., Stepankova, V., Chaloupkova, R., Brezovsky, J., Prokop, Z., Damborsky, J.: Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization., ACS Catalysis, DOI:10.1021/acscatal.7b03523., 2018.

Sumbalova, L., Stourac, J., Martinek, T., Bednar, D., Damborsky, J.: 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, 2018.

Kaushik, S., Marques, S. M., Khirsariya, P., Paruch, K., Libichova, L., Brezovsky, J., Prokop, Z., Chaloupkova, R., Damborsky, J.: Impact of the Access Tunnel Engineering on Catalysis is Strictly Ligand-Specific., FEBS Journal, 285, 1456-1476, 2018.

Marques, S. M., Bednar, D., Damborsky, J.: Computational Study of Protein-Ligand Unbinding for Enzyme Engineering, Frontiers in Chemistry, 6, 650, 2018.

Kokkonen, P., Sykora, J., Prokop, Z., Ghose, A., Bednar, D., Amaro, M., Bidmanova, S., Beerens, K., Damborsky, J., Hof, M.: Molecular Gating of an Engineered Enzyme Captured in Real Time, Journal of the American Chemical Society, 140, 17999–18008, 2018.

Kokkonen, P., Bednar, D., Dockalova, V., Prokop, Z., Damborsky, J.: 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, 2018.

2017

Kaushik, S., Prokop, Z., Damborský, J., Chaloupková, R.: Kinetics of Binding of Fluorescent Ligands to Enzymes with Engineered Access Tunnels, FEBS Journal, in press, 2017.

Buryska, T., Babkova, P., Vavra, O., Damborsky, J., Prokop, Z.: A Haloalkane Dehalogenase From a Marine Microbial Consortium Possessing Exceptionally Broad Substrate Specificity., Applied and Environmental Microbiology, 84, e01684-17, 2017.

Marques, S. M., Dunajova, Z., Prokop, Z., Chaloupkova, R., Brezovsky, J., Damborsky, J.: Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling., Journal of Chemical Information and Modeling, 57, 1970-1989, 2017.

Vad, V. , Byska, J., Jurcik, A., Viola, I. , Groller, E. M., Hauser, H., Marques, S. M., Damborsky, J., Kozlikova, B. : Watergate: Visual Exploration of Water Trajectories in Protein Dynamics., Eurographics Workshop on Visual Computing for Biology and Medicine Proceedings, 36, 33-42, 2017.

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.: NewProt – a Protein Engineering Portal., Protein Engineering, Design & Selection, 30, 441-447, 2017.

Liskova, V., Stepankova, V., Bednar, D., Brezovsky, J., Prokop, Z., Chaloupkova, R., Damborsky, J.: 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, 2017.

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.

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	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. : CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories., Bioinformatics, bty386, 2018.
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]
CaverDock	Vavra, O., Filipovic, J., Plhak, J., Bednar, D., Marques, S., Brezovsky, J., Pavelka, A., Matyska, L., Damborsky, J.: CAVERDOCK: A New Tool for Analysis of Ligand Binding and Unbinding Based on Molecular Docking, In preparation, 2018.

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