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VKCDB：电压门控钾通道数据库。

VKCDB: voltage-gated potassium channel database.

作者信息

Li Bin, Gallin Warren J

机构信息

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

出版信息

BMC Bioinformatics. 2004 Jan 9;5:3. doi: 10.1186/1471-2105-5-3.

DOI:10.1186/1471-2105-5-3
PMID:14715090
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC317694/
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 (Voltage-gated potassium [K] Channel DataBase) 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.

摘要

背景

电压门控钾通道家族由一组功能多样的膜蛋白组成。它们有助于维持和调节基于钾离子的膜电位成分，因此对许多关键生理过程至关重要。VKCDB（电压门控钾[K]通道数据库）是这些通道的结构和功能数据的数据库。它被设计为研究电压门控钾通道功能分子基础的资源。

描述

通过使用BLASTP搜索GENBANK和SWISSPROT来识别电压门控钾通道序列。对所有电压门控钾通道的注释进行了选择性解析并整合到VKCDB中。通道的电生理和药理学数据从已发表的期刊文章中收集。每个VKCDB条目都包含通过TMHMM和PHD进行的跨膜结构域预测。还包括四个Kv家族和KCNQ家族通道保守结构域的多序列比对。目前VKCDB包含346个通道条目。可以使用一组功能相关类别进行浏览和搜索。也可以使用本地BLAST引擎搜索蛋白质序列。

结论

VKCDB是用于电压门控钾通道比较研究的资源。构建VKCDB所使用的方法具有通用性；它们可用于为其他蛋白质家族创建专门的数据库。可通过http://vkcdb.biology.ualberta.ca访问VKCDB。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0264/317694/14100951ebf3/1471-2105-5-3-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0264/317694/e8d1646b795a/1471-2105-5-3-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0264/317694/14100951ebf3/1471-2105-5-3-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0264/317694/e8d1646b795a/1471-2105-5-3-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0264/317694/14100951ebf3/1471-2105-5-3-2.jpg

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