A Protein Tertiary Structure Search System

Seiichi Aikawa
Mayumi Tomikawa
Fumiko Matsuzawa

Fujitsu Laboratories Ltd.


We have developed the system which searches for similar tertiary stuctures to analyze relationship between protein function and its structural similarity. This system adopted root mean square distance to judge structural similarity, and generates an interpretation tree, which represents a set of pairings of elements between structures, and prunes it based on geometric constraints. We tried to search for similar stuctures of ATP/GTP binding sites from PDB. As a result, collected similar structures had same function. Experimental result suggests this method is useful for this kind of research.