Searches for Topologically and Three Dimensionally Similar Structures in Proteins

Kenji Satou[1] (ken@csce.kyushu-u.ac.jp)
Emiko Furuichi[2] (emi@grt.kyushu-u.ac.jp)
Satoru Kuhara[3] (kuhara@grt.kyushu-u.ac.jp)
Toshihisa Takagi[4] (takagi@ims.u-tokyo.ac.jp)

[1] Department of Computer Science and Communication Engineering, Kyushu University
Hakozaki, Higashi-ku, Fukuoka 812, Japan
[2] Fukuoka Women's Junior College, Gojo, Dazaifu, Fukuoka 818-01, Japan
[3] Graduate School of Genetic Resources Technology, Kyushu University
Hakozaki, Higashi-ku, Fukuoka 812, Japan
[4]Human Genome Center, Institute of Medical Science, The University of Tokyo
Shiroganedai, Minato-ku, Tokyo 108, Japan

Abstract

We developed a deductive database system PACADE for analyzing three dimensional and secondary structures of protein. PACADE is equipped with a function to search for similar structures in proteins. Unlike other approaches based on calculation of the inter-atomic root mean square distance, this function is based on logic programming and source level rule rewriting techniques.

We describe herein the result of searches for topologically similar structures and three dimensionally similar ones. A user of PACADE can select these two levels of similarities by adding/deleting prefixes.