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AAindex: amino acid index database, progress report 2008.

Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M - Nucleic Acids Res. (2007)

Bottom Line: AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku Tokyo 108-8639, Japan. shuichi@hgc.jp

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/).

Show MeSH
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).
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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).

Mentions: To represent an overview of the relationships among current amino acids indices, we constructed the minimum spanning tree of amino acid indices by the procedure described by Tomii et al. (2) (Figure 1). In Figure 1, each rectangle represents an index. The colored rectangles are the 402 indices classified in six groups defined by Tomii and coworkers. The indices belonging to the Tomii's classification are still grouped into clusters. Newly added indices are distributed evenly across the tree. That is, the indices for various kinds of properties have been added to the AAindex.Figure 1.


AAindex: amino acid index database, progress report 2008.

Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M - Nucleic Acids Res. (2007)

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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238890&req=5

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).
Mentions: To represent an overview of the relationships among current amino acids indices, we constructed the minimum spanning tree of amino acid indices by the procedure described by Tomii et al. (2) (Figure 1). In Figure 1, each rectangle represents an index. The colored rectangles are the 402 indices classified in six groups defined by Tomii and coworkers. The indices belonging to the Tomii's classification are still grouped into clusters. Newly added indices are distributed evenly across the tree. That is, the indices for various kinds of properties have been added to the AAindex.Figure 1.

Bottom Line: AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku Tokyo 108-8639, Japan. shuichi@hgc.jp

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/).

Show MeSH