Detection method of function site of proteins by the finding of amino acid residues at the similar three dimensional positions (5): Quantitative evaluation of the results by Herfindahl index.

Abstract

It is important problem in a protein science to detect active sites on protein structures. Some automatic detection methods has been presented as follows; finding a similar structure to known protein active sites, finding pockets and/or cavities on protein surfaces, and so on. We already proposed a method to detect amino acid residues, which construct a function site, using the similarity in 3-D structure of same function proteins. By the last report we clarified the scope and limits of this method. In this report, we applied Herfindahl index, which generally uses in economics parameter, as an indicator of variety of extracted amino acid residues as function site. The index values are obtained in all pairs of 10 serine proteases. The pair, which extracts reasonable amino acid residues, gives high index score and the other pair, which does not give those residues, gives low one. By comparing the index scores and detection validity, which found in previous study, it is found that the method could be detect the true active site residues in the case of more than 450 in index score.