Construction of a Three-Dimensional Protein Motif Database (2)

Abstract

Structural feature analysis or similarity analysis of proteins provides us a lot of useful information for better understanding of molecular biological science and the related areas. In PROSITE database, a structural feature called motif is usually defined by a pattern of amino acid sequence using regular expressions. In our preceding works, we have constructed a 3D protein motif database that corresponded to the PROSITE. In this database, various 3D substructures that have common sequence pattern are found by visual checking. In this paper, we have investigated a classification method for such substructures. That is, a dissimilarity criterion for a pair of substructures is defined and a classification is done using a dissimilarity matrix for a group of 3D substructures. Then a substructure that has the smallest sum of dissimilarity value is defined as a representative 3D pattern. The result of 3D motif search using these representative patterns of also discussed.