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

TLDR

Studying transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to understanding their biological function, and detailed analysis of structural features influencing these paths is important for engineering proteins for biomedical and biotechnological applications. CAVER Analyst 2.0 uses novel integrated algorithms for efficient analysis and data reduction in large protein structures and molecular dynamics simulations, and is available as a multi‑platform standalone Java‑based application. CAVER Analyst 2.0 is a software tool that provides quantitative analysis and real‑time visualization of tunnels and channels in static and dynamic structures, offering many new functions such as advanced techniques for intuitive visual inspection of their spatiotemporal behavior. Binaries, documentation, and supplementary data are freely available at www.caver.cz and Bioinformatics online.

Abstract

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.