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

Barbora Kozlikova; Eva Sebestova; Vilem Sustr; Jan Brezovsky; Ondrej Strnad; Lukas Daniel; David Bednar; Antonin Pavelka; Martin Manak; Martin Bezdeka; Petr Benes; Matus Kotry; Artur Gora; Jiri Damborsky; Jiri Sochor

doi:10.1093/bioinformatics/btu364

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

Bioinformatics. 2014 Sep 15;30(18):2684-5. doi: 10.1093/bioinformatics/btu364. Epub 2014 May 29.

Authors

Affiliations

¹ 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.
² 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.

PMID: 24876375
DOI: 10.1093/bioinformatics/btu364

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites
Computational Biology / methods*
Computer Graphics*
Ligands
Proteins / chemistry*
Proteins / metabolism
Software*
User-Computer Interface

Substances

Ligands
Proteins