AAindex: amino acid index database, progress report 2008 - PubMed (original) (raw)

. 2008 Jan;36(Database issue):D202-5.

doi: 10.1093/nar/gkm998. Epub 2007 Nov 12.

Affiliations

• PMID: 17998252
• PMCID: PMC2238890
• DOI: 10.1093/nar/gkm998

AAindex: amino acid index database, progress report 2008

Shuichi Kawashima et al. Nucleic Acids Res. 2008 Jan.

Abstract

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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Figures

Figure 1.

The minimum spanning tree of the amino acid indices stored in the AAindex1 release 9.0. Each rectangle is an amino acid index. Colored nodes represent the indices classified by Tomii et al. (2) Red: alpha and turn propensities, Yellow: beta propensity, Green: composition, Blue: hydrophobicity, Cyan: physicochemical properties, Gray: other properties. White: the indices added to the AAindex after the release 3.0 by Tomii et al. (2).

Figure 2.

An example of database entry in the AAindex3. Each record of an entry is identified by the one-letter codes: H, accession number; D, definition of the entry; R, PMID identifier; A, author(s); T, title of the journal article; J, journal citation information; M, actual data in the specified order.

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