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

Yukiko Tsukamoto | Zendy; Kingo Takiguchi | Zendy; Kenji Satou | Zendy; Emiko Furuichi | Zendy; Toshiyuki Takagi | Zendy; Satoru Kuhara | Zendy

Open Access

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

Author(s) -

Yukiko Tsukamoto,

Kingo Takiguchi,

Kenji Satou,

Emiko Furuichi,

Toshiyuki Takagi,

Satoru Kuhara

Publication year - 1997

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/13.2.183

Subject(s) - computer science , deductive database , inference , similarity (geometry) , protein structure database , function (biology) , data mining , protein structure , data structure , topology (electrical circuits) , theoretical computer science , information retrieval , artificial intelligence , mathematics , programming language , chemistry , biology , combinatorics , sequence database , evolutionary biology , gene , biochemistry , image (mathematics)

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.

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