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CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.

ABSTRACT: Motivation:Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. Results:CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. Availability and implementation:CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Jurcik A 

PROVIDER: S-EPMC6184705 | biostudies-other | 2018 Oct

REPOSITORIES: biostudies-other

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CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.

Jurcik Adam A   Bednar David D   Byska Jan J   Marques Sergio M SM   Furmanova Katarina K   Daniel Lukas L   Kokkonen Piia P   Brezovsky Jan J   Strnad Ondrej O   Stourac Jan J   Pavelka Antonin A   Manak Martin M   Damborsky Jiri J   Kozlikova Barbora B  

Bioinformatics (Oxford, England) 20181001 20

<h4>Motivation</h4>Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications.<h4>Results</h4>CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels an  ...[more]

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