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

• Published in: Nucleic acids research 2019-07, Vol.47 (W1), p.W414-W422
• Main Authors: Stourac, Jan, Vavra, Ondrej, Kokkonen, Piia, Filipovic, Jiri, Pinto, Gaspar, Brezovsky, Jan, Damborsky, Jiri, Bednar, David
• Format: Article
• Language: English
• Subjects: Algorithms; Amino Acid Sequence; Animals; Benchmarking; Binding Sites; Carrier Proteins - chemistry; Carrier Proteins - metabolism; Computational Biology - methods; Humans; Internet; Ligands; Molecular Docking Simulation; Protein Binding; Protein Interaction Domains and Motifs; Protein Structure, Quaternary; Protein Structure, Tertiary; User-Computer Interface; Web Server Issue
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkz378

Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels, and study of the ligands' transport through these transport pathways. Caver Web is the first interactive tool allowing both the analyses within a single graphical user interface. The server is built on top of the abundantly used tunnel detection tool Caver 3.02 and CaverDock 1.0 enabling the study of the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for a tunnel identification and a list of ligands for the transport analysis. The automated guidance procedures assist the users to set up the calculation in a way to obtain biologically relevant results. The identified tunnels, their properties, energy profiles and trajectories for ligands' passages can be calculated and visualized. The tool is very fast (2-20 min per job) and is applicable even for virtual screening purposes. Its simple setup and comprehensive graphical user interface make the tool accessible for a broad scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.