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

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. Graphical Abstract

Automated summary

ChannelsDB 2.0 is an updated database that provides structural information about the position, geometry, and physicochemical properties of protein channels and pores. It incorporates data calculated by CAVER and MOLE tools, as well as additional information from AlphaFill database, resulting in significantly expanded channel annotations. The database stores information such as geometrical features and physico-chemical properties based on channel-lining amino acids, and is interlinked with UniProt mutation annotation data. ChannelsDB 2.0 serves as an important resource for in-depth analysis of the role of biomacromolecular tunnels and pores.