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 34: 3586-3588 (2018)

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: CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz.

Full text •  Supplement

Citation

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., 2018: CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics 34: 3586-3588.

Martin to Present at ProtStab’2021
Nikola’s Success at SOC
The Dean’s Award for Jan
Gaspar Presented at 18th IUGEN International Winter School
Event Biotechnology Innovations for the Cosmetic Industry
David Presented at ESAB Webinar
Poster Award for Andrea