ChannelsDB: database of biomacromolecular tunnels and pores

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Title in English ChannelsDB: Database of biomacromolecular tunnels and pores
Authors

PRAVDA Lukáš SEHNAL David SVOBODOVÁ VAŘEKOVÁ Radka NAVRÁTILOVÁ Veronika TOUŠEK Dominik BERKA Karel OTYEPKA Michal KOČA Jaroslav

Type Article in Periodical
Magazine / Source Nucleic Acids Research
MU Faculty or unit

Central European Institute of Technology

Citation
Web http://dx.doi.org/10.1093/nar/gkx868
Doi http://dx.doi.org/10.1093/nar/gkx868
Field Biochemistry
Keywords protein structure; protein channel; substrate channeling; tunnel; pore; MOLE; database; CYP P450; ribosome; aquaporin
Attached files
Description 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.
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