AAindex database

Figure 5.7. Amino acid index databases for physicochemical properties. The physicochemical properties, conformational parameters, and mutational indexes can be retrieved from AAindex database using keyword search.

Physicochemical properties of amino acids are very useful descriptors for understanding the structures and properties of proteins. These properties are expressed numerically in indexes that can be retrieved from the AAindex database. Design an index database of physicochemical properties of amino acids with Microsoft Access that may facilitate the data retrieval according to their chemical similarities ... 

The physico-chemical properties of amino acids are summarized in Table 1. This includes a wide array of measiues, from refractivity and melting point to the pKa at the amino group. Some of the parameters span a narrow range of values (e.g., the molecular weights and melting points). Other parameters differ by a factor of 100-fold or more, which include the pKas at the amino group and solubility. The AAindex database compiled by Kawashima et al. (21) is an excellent soiuce of additional information that concerns the physico-chemical properties of amino acids. 

One of the most comprehensive resources of amino acid properties freely available on line is the amino acid index database (AAindex), which includes numerical indices representing various physico-chemical, biochemical, and statistical properties of amino acids and pairs of amino acids. AAindex database has been made publicly available by the Japanese GenomeNet database service (http //www.genome.jp/aaindex/). 

PDB at RCSB ReadSeq SMILES tutorial TOPS cartoons AAindex Parameters for amino acids BioMagResBank (BMRB) EBLSequences of proteins/ncleic acids Entrez Sequences of proteins/nucleic acids European Large Subunit rRNA Database European Small Subunit rRNA Database GlycoSuiteDB... 

Kawashima S, Ogata H, Kanehisa M. AAindex amino acid index database. Nucl. Acids Res. 1999 27 368-369. 

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