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Nucleic Acids Research Advance Access published online on October 8, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn672
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

TMFunction: database for functional residues in membrane proteins

M. Michael Gromiha1,*, Yukimitsu Yabuki1, M. Xavier Suresh1, A. Mary Thangakani2, Makiko Suwa1 and Kazuhiko Fukui1

1Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064 and 2Advanced Technology Inc., Tokyo, Japan

*To whom correspondence should be addressed. Tel: +81 3 3599 8046; Fax: +81 3 3599 8081; Email: michael-gromiha{at}aist.go.jp

Received August 13, 2008. Revised September 22, 2008. Accepted September 22, 2008.

We have developed the database TMFunction, which is a collection of more than 2900 experimentally observed functional residues in membrane proteins. Each entry includes the numerical values for the parameters IC50 (measure of the effectiveness of a compound in inhibiting biological function), Vmax (maximal velocity of transport), relative activity of mutants with respect to wild-type protein, binding affinity, dissociation constant, etc., which are important for understanding the sequence–structure–function relationship of membrane proteins. In addition, we have provided information about name and source of the protein, Uniprot and Protein Data Bank codes, mutational and literature information. Furthermore, TMFunction is linked to related databases and other resources. We have set up a web interface with different search and display options so that users have the ability to get the data in several ways. TMFunction is freely available at http://tmbeta-genome.cbrc.jp/TMFunction/.


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