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CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures

Kozlikova, Barbora
Author Kozlikova, Barbora Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Sebestova, Eva
Author Sebestova, Eva Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Sustr, Vilem
Author Sustr, Vilem Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Brezovsky, Jan
Author Brezovsky, Jan Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Strnad, Ondrej
Author Strnad, Ondrej Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Daniel, Lukas
Author Daniel, Lukas Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Bednar, David
Author Bednar, David Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Pavelka, Antonin
Author Pavelka, Antonin Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Manak, Martin
Author Manak, Martin Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Bezdeka, Martin
Author Bezdeka, Martin Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Benes, Petr
Author Benes, Petr Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Kotry, Matus
Author Kotry, Matus Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Gora, Artur
Author Gora, Artur Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Damborsky, Jiri
Author Damborsky, Jiri Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic
Sochor, Jiri
Author Sochor, Jiri Department of Computer Graphics and Design, Human Computer Interaction Laboratory, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno and Department of Computer Science and Engineering, Faculty of Applied Sciences, University of West Bohemia, Univerzitni 8, 306 14 Plzen, Czech Republic

Bioinformatics (Oxford, England). 2014 Sep 15 ; 30 (18) : 2684-5. [epub] 20140529

Bioinformatics
ISSN 1367-4811 | 1367-4803
Source

Language English Country England, Great Britain Media print-electronic

Document type Journal Article, Research Support, Non-U.S. Gov't

Persistent link https://www.medvik.cz/link/pmid24876375

PubMed 24876375
DOI 10.1093/bioinformatics/btu364
PII: btu364
Knihovny.cz E-resources

UNLABELLED: The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. AVAILABILITY AND IMPLEMENTATION: CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at http://www.caver.cz.

Department of Computer Graphics and Design Human Computer Interaction Laboratory Faculty of Informatics Masaryk University Botanicka 68a 602 00 Brno Loschmidt Laboratories Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX Faculty of Science Masaryk University Kamenice 5 A13 625 00 Brno and Department of Computer Science and Engineering Faculty of Applied Sciences University of West Bohemia Univerzitni 8 306 14 Plzen Czech Republic Department of Computer Graphics and Design Human Computer Interaction Laboratory Faculty of Informatics Masaryk University Botanicka 68a 602 00 Brno Loschmidt Laboratories Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX Faculty of Science Masaryk University Kamenice 5 A13 625 00 Brno and Department of Computer Science and Engineering Faculty of Applied Sciences University of West Bohemia Univerzitni 8 306 14 Plzen Czech Republic

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