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Nucleic Acids Research Advance Access published online on November 12, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm998
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© 2007 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

AAindex: amino acid index database, progress report 2008

Shuichi Kawashima1,*, Piotr Pokarowski2, Maria Pokarowska3, Andrzej Kolinski4, Toshiaki Katayama1 and Minoru Kanehisa1,5

1Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku Tokyo 108-8639, Japan, 2Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, Warsaw University, 02-097 Warsaw, 3Faculty of Geodesy and Cartography, Warsaw University of Technology, 00-661 Warsaw, 4Laboratory of Theory of Biopolymers, Faculty of Chemistry, Warsaw University, 02-093 Warsaw, Poland and 5Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan

*To whom correspondence should be addressed. Tel: +81 3 5449 5611; Fax: +81 3 5449 5434; Email: shuichi{at}hgc.jp

Received September 15, 2007. Revised October 19, 2007. Accepted October 22, 2007.

AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. We have added a collection of protein contact potentials to the AAindex as a new section. Accordingly AAindex consists of three sections now: AAindex1 for the amino acid index of 20 numerical values, AAindex2 for the amino acid substitution matrix and AAindex3 for the statistical protein contact potentials. All data are derived from published literature. The database can be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.jp/dbget-bin/www_bfind?aaindex) or downloaded by anonymous FTP (ftp://ftp.genome.jp/pub/db/community/aaindex/).


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