ChannelsDB: database of biomacromolecular tunnels and pores

Nucleic Acids Res. 2018 Jan 4;46(D1):D399-D405. doi: 10.1093/nar/gkx868.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry*
  • Amino Acids / metabolism
  • Animals
  • Catalytic Domain
  • Coenzymes / chemistry
  • Coenzymes / metabolism
  • Cytochrome P-450 CYP2D6 / chemistry*
  • Cytochrome P-450 CYP2D6 / genetics
  • Cytochrome P-450 CYP2D6 / metabolism
  • Databases, Protein*
  • Eukaryotic Cells / cytology
  • Eukaryotic Cells / enzymology
  • Gene Expression
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Ion Channels / chemistry*
  • Ion Channels / genetics
  • Ion Channels / metabolism
  • Mutation
  • Nuclear Pore / chemistry*
  • Nuclear Pore / genetics
  • Nuclear Pore / metabolism
  • Prokaryotic Cells / cytology
  • Prokaryotic Cells / enzymology
  • Software*
  • Static Electricity


  • Amino Acids
  • Coenzymes
  • Ion Channels
  • Cytochrome P-450 CYP2D6