ChannelsDB: database of biomacromolecular tunnels and pores. Issue Volume 46:Issue D1(2018) (3rd October 2017)

• Record Type: Journal Article
• Authors: Pravda, Lukáš; Sehnal, David; Svobodová Vařeková, Radka; Navrátilová, Veronika; Toušek, Dominik; Berka, Karel; Otyepka, Michal; Koča, Jaroslav
• Is Part Of: Nucleic acids research. Volume 46:Issue D1(2018)
• Page Start: D399
• Page End: D405
• Publication Date: 2017-10-03
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkx868
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: ChannelsDB (http://ncbr.muni.cz/ChannelsDB ) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.