Development of Software Tools to Construct a 3D Motif Dictionary of Proteins

Hiroaki KATO*, Hiroyuki MIYATA, Naohiro UCHIMURA, Yoshimasa TAKAHASHI and Hidetsugu ABE

Dept. of Knowledge-based Information Engineering, Toyohashi University of Technology
1-1 Hibarigaoka, Tenpaku-cho, Toyohashi, Aichi 441-8580, Japan

(Received: March 30, 2004; Accepted for publication: May 18, 2004; Published on Web: August 10, 2004)

This paper describes a three-dimensional (3D) protein motif dictionary system that is closely related to the PROSITE sequence motifs. Because there were many different 3D motif patterns but having a particular PROSITE sequence pattern, we have investigated the approaches for quantitative comparison and clustering of such 3D structure segments. For a pair of 3D structure segments, the dissimilarity value was defined with the root mean squares of inter-residue distances. A conformational pattern clustering was employed for grouping the 3D patterns on the basis of the dissimilarity matrix. Some additional knowledge information described in PROSITE was also used to refine the clustering results. A 3D motif dictionary was constructed using all the data set of the Protein Data Bank. A graphical user interface for using the dictionary was also developed.

Keywords: Protein motif, 3D structural feature, Structural similarity, 3D motif dictionary, PROSITE


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