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      AAindex: amino acid index database, progress report 2008

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          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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          AAindex: amino acid index database.

          S Kawashima (2000)
          AAindex is a database of amino acid indices and amino acid mutation matrices. An amino acid index is a set of 20 numerical values representing various physico--chemical and biochemical properties of amino acids. An amino acid mutation matrix is generally 20 x 20 numerical values representing similarity of amino acids. AAindex consists of two sections: AAindex1 for the collection of published amino acid indices and AAindex2 for the collection of published amino acid mutation matrices. Each entry of either AAindex1 or AAindex2 consists of the definition, the reference information, a list of related entries in terms of the correlation coefficient and the actual data. The database may be accessed through the DBGET/LinkDB system at GenomeNet (http://www. genome.ad.jp/aaindex/ ) or may be downloaded by anonymous FTP (ftp://ftp.genome.ad.jp/db/genomenet/aaindex/ ).
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            AAindex: Amino Acid Index Database.

            M Kanehisa, S Kawashima, Yukio Ogata (1999)
            AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. It consists of two sections: AAindex1 for the amino acid index of 20 numerical values and AAindex2 for the amino acid mutation matrix of 210 numerical values. Each entry of either AAindex1 or AAindex2 consists of the definition, the reference information, a list of related entries in terms of the correlation coefficient, and the actual data. The database may be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.ad. jp/dbget/) or may be downloaded by anonymous FTP (ftp://ftp.genome. ad.jp/db/genomenet/aaindex/).
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              Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins.

              M Kanehisa, K Tomii (1995)
              An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biochemical properties of amino acids. As a follow-up to the previous study, we have increased the size of the database, which currently contains 402 published indices, and re-performed the single-linkage cluster analysis. The results basically confirmed the previous findings. Another important feature of amino acids that can be represented numerically is the similarity between them. Thus, a similarity matrix, also called a mutation matrix, is a set of 20 x 20 numerical values used for protein sequence alignments and similarity searches. We have collected 42 published matrices, performed hierarchical cluster analyses and identified several clusters corresponding to the nature of the data set and the method used for constructing the mutation matrix. Further, we have tried to reproduce each mutation matrix by the combination of amino acid indices in order to understand which properties of amino acids are reflected most. There was a relationship between the PAM units of Dayhoff's mutation matrix and the volume and hydrophobicity of amino acids. The database of 402 amino acid indices and 42 amino acid mutation matrices is made publicly available on the Internet.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): January 2008
                Publication date (Electronic): 12 November 2007
                Publication date PMC-release: 12 November 2007
                Volume: 36
                Issue: Database issue , Database issue
                Pages: D202-D205
                Affiliations
                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
                Author notes
                *To whom correspondence should be addressed.+81 3 5449 5611+81 3 5449 5434 shuichi@ 123456hgc.jp
                Article
                DOI: 10.1093/nar/gkm998
                PMC ID: 2238890
                PubMed ID: 17998252
                SO-VID: 94c59993-fe4e-4abd-a0ba-8d25a8a988b2
                Copyright © © 2007 The Author(s)
                License:

                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.

                History
                Date received : 15 September 2007
                Date revision received : 19 October 2007
                Date accepted : 22 October 2007
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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