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AAindex: Amino Acid Index Database

S Kawashima1, H Ogata, M Kanehisa

  • 1Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

Nucleic Acids Research
|December 10, 1998
PubMed
Summary
This summary is machine-generated.

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AAindex is a comprehensive database detailing amino acid properties and mutations. This resource provides numerical indices for physicochemical and biochemical characteristics, aiding biological research.

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • Amino acids are fundamental building blocks of proteins.
  • Understanding amino acid properties is crucial for predicting protein structure and function.
  • Databases that compile these properties facilitate large-scale biological research.

Purpose of the Study:

  • To present AAindex, a database of numerical indices for amino acid properties.
  • To provide access to data on physicochemical and biochemical characteristics of amino acids and their mutations.

Main Methods:

  • AAindex is structured into two sections: AAindex1 for individual amino acid indices and AAindex2 for mutation matrices.
  • Each entry includes definitions, reference information, correlation coefficients for related entries, and the actual numerical data.

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  • Data is accessible via the DBGET/LinkDB system at GenomeNet and downloadable via anonymous FTP.

    • Main Results:

    • The database contains numerical representations of various amino acid properties.
    • It includes indices for 20 amino acids and mutation matrices for 210 pairs.
    • Information on related entries based on correlation coefficients is provided.

    Conclusions:

    • AAindex serves as a valuable resource for researchers studying protein structure, function, and evolution.
    • The database facilitates quantitative analysis of amino acid properties and their implications in biological systems.