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Open Access Highly Accessed Database

VKCDB: Voltage-gated potassium channel database

Bin Li and Warren J Gallin*

Author Affiliations

Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada

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BMC Bioinformatics 2004, 5:3  doi:10.1186/1471-2105-5-3

Published: 9 January 2004

Abstract

Background

The family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins. They help maintain and regulate the potassium ion-based component of the membrane potential and are thus central to many critical physiological processes. VKCDB (

    V
oltage-gated potassium [
    K
]
    C
hannel
    D
ata
    B
ase) is a database of structural and functional data on these channels. It is designed as a resource for research on the molecular basis of voltage-gated potassium channel function.

Description

Voltage-gated potassium channel sequences were identified by using BLASTP to search GENBANK and SWISSPROT. Annotations for all voltage-gated potassium channels were selectively parsed and integrated into VKCDB. Electrophysiological and pharmacological data for the channels were collected from published journal articles. Transmembrane domain predictions by TMHMM and PHD are included for each VKCDB entry. Multiple sequence alignments of conserved domains of channels of the four Kv families and the KCNQ family are also included. Currently VKCDB contains 346 channel entries. It can be browsed and searched using a set of functionally relevant categories. Protein sequences can also be searched using a local BLAST engine.

Conclusions

VKCDB is a resource for comparative studies of voltage-gated potassium channels. The methods used to construct VKCDB are general; they can be used to create specialized databases for other protein families. VKCDB is accessible at http://vkcdb.biology.ualberta.ca webcite.