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© Oxford University Press

Application of a deductive database system to search for topological and similar three-dimensional structures in protein

Y. Tsukamoto 1,4, K. Takiguchi 1,5, K. Satou 2, E. Furuichi 3, T. Takagi 2 and S. Kuhara 1,6

1Graduate School of Genetic Resources Technology, Kyushu University Hakozaki, Higashi-ku, Fukuoka 812, Japan yukiko{at}grt.kyushu-u.ac.jp ken{at}ims.u-tokyo.ac.jp kuhara{at}grt.kyushu-u.ac.jp
2Human Genome Center, Institute of Medical Science, University of Tokyo Shiroganedai, Minato-ku, Tokyo 108, Japan takagi{at}ims.u-tokyo.ac.jp
3Fukuoka Women's Junior College Gojo Dazaifu, Fukuoka 818-01, Japan emiko{at}grt.kyushu-u.ac.jp

6To whom correspondence should be addressed

A deductive database system PACADE (Protein Atomic Coordinate Analyzer with Deductive Engine) has been developed for protein structure analysis. With this system, super-secondary structures described in logical and declarative rules can be retrieved effectively. For protein structure analysis, comparison of local structures in different proteins is a necessary mean. A function to search for similar structures has, therefore, been added to the PACADE system. We describe herein the result of searches for the same topological structures and three-dimensionally similar ones. A user of PACADE can select these two levels of similarity by changing parameters. This function enables the inference system to retrieve similar structures, according to the restraints of variables defined by the user. Similar super-secondary structures among proteins can be searched for automatically, which is useful for protein structure analysis. The retrieved similar super-secondary structures can serve as criteria for protein spatial alignment.

Received on August 30, 1996; accepted on November 28, 1996

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