ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era

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Authors

ŠPAČKOVÁ Anna VÁVRA Ondřej RAČEK Tomáš BAZGIER Václav SEHNAL David DAMBORSKÝ Jiří SVOBODOVÁ Radka BEDNÁŘ David BERKA Karel

Year of publication 2024
Type Article in Periodical
Magazine / Source Nucleic Acids Research
MU Faculty or unit

Faculty of Science

Citation
Web https://doi.org/10.1093/nar/gkad1012
Doi http://dx.doi.org/10.1093/nar/gkad1012
Keywords amino acids; databases; protein; software; biomacromolecules; 3D structure; organelle- and cell-sized models; visualization
Attached files
Description ChannelsDB 2.0 is an updated database providing structural information about the position, geometry and physicochemical properties of protein channels-tunnels and pores-within deposited biomacromolecular structures from PDB and AlphaFoldDB databases. The newly deposited information originated from several sources. Firstly, we included data calculated using a popular CAVER tool to complement the data obtained using original MOLE tool for detection and analysis of protein tunnels and pores. Secondly, we added tunnels starting from cofactors within the AlphaFill database to enlarge the scope of the database to protein models based on Uniprot. This has enlarged available channel annotations similar to 4.6 times as of 1 September 2023. The database stores information about geometrical features, e.g. length and radius, and physico-chemical properties based on channel-lining amino acids. The stored data are interlinked with the available UniProt mutation annotation data. ChannelsDB 2.0 provides an excellent resource for deep analysis of the role of biomacromolecular tunnels and pores. The database is available free of charge: https:////channelsdb2.biodata.ceitec.cz.
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