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