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Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport
J. Stourac, O. Vavra, P. Kokkonen, J. Filipovic, G. Pinto, J. Brezovsky, J. Damborsky, D. Bednar,
Language English Country Great Britain
Document type Journal Article, Research Support, Non-U.S. Gov't
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PubMed
31114897
DOI
10.1093/nar/gkz378
Knihovny.cz E-resources
- MeSH
- Algorithms * MeSH
- Benchmarking MeSH
- Protein Interaction Domains and Motifs MeSH
- Internet MeSH
- Protein Structure, Quaternary MeSH
- Humans MeSH
- Ligands MeSH
- Amino Acid Sequence MeSH
- Molecular Docking Simulation MeSH
- Protein Structure, Tertiary MeSH
- Carrier Proteins chemistry metabolism MeSH
- User-Computer Interface * MeSH
- Protein Binding MeSH
- Binding Sites MeSH
- Computational Biology methods MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
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.
References provided by Crossref.org
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