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.

Department of Computer Graphics and Design Human Computer Interaction Laboratory Faculty of Informatics Masaryk University Brno Czech Republic

Department of Gene Expression Institute of Molecular Biology and Biotechnology Faculty of Biology Adam Mickiewicz University Poznan Poland

International Centre for Clinical Research St Anne's University Hospital Brno Czech Republic

International Institute of Molecular and Cell Biology in Warsaw Warsaw Poland

Loschmidt Laboratories Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment Faculty of Science Masaryk University Brno Czech Republic

NTIS New Technologies for the Information Society Faculty of Applied Sciences University of West Bohemia Pilsen Czech Republic

Visualization Group Department of Informatics University of Bergen Bergen Norway

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Silencing sensory neuron membrane protein RferSNMPu1 impairs pheromone detection in the invasive Asian Palm Weevil

Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling

Engineering the protein dynamics of an ancestral luciferase

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Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport