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

ABSTRACT: 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 ∼4.6 times as of 1 September 2023. The database stores information about geometrical features, e.g. leng

SUBMITTER: Spackova A 

PROVIDER: S-EPMC10767935 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature