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Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

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AAindex: amino acid index database, progress report 2008.

Shuichi Kawashima¹, Piotr Pokarowski, Maria Pokarowska

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. shuichi@hgc.jp

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Summary

This summary is machine-generated.

The AAindex database now includes protein contact potentials, expanding its resources on amino acid properties. This updated database aids research in protein structure and function analysis.

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Area of Science:

Biochemistry
Bioinformatics
Structural Biology

Background:

The AAindex database compiles numerical indices for amino acid physicochemical and biochemical properties.
Existing sections include AAindex1 (amino acid indices) and AAindex2 (substitution matrices).

Purpose of the Study:

To augment the AAindex database with a new section dedicated to protein contact potentials.
To provide researchers with a comprehensive resource for amino acid and protein interaction data.

Main Methods:

Data compilation from published scientific literature.
Integration of statistical protein contact potentials into the AAindex framework.
Inclusion of AAindex3 for statistical protein contact potentials.

Main Results:

AAindex now comprises three distinct sections: AAindex1, AAindex2, and the newly added AAindex3.
The database offers a unified resource for amino acid indices, substitution matrices, and protein contact potentials.
All data is sourced from peer-reviewed publications.

Conclusions:

The expanded AAindex database offers a more comprehensive resource for researchers studying protein properties and interactions.
Accessibility is provided through GenomeNet's DBGET/LinkDB system and anonymous FTP.
This enhancement supports advancements in bioinformatics and structural biology research.