Y Tsukamoto, K Takiguchi, K Satou, E Furuichi, T Takagi, S Kuhara
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引用次数: 9
摘要
开发了一个用于蛋白质结构分析的演绎数据库系统PACADE (Protein Atomic Coordinate Analyzer with deduction Engine)。利用该系统,可以有效地检索用逻辑和声明性规则描述的超二级结构。在蛋白质结构分析中,比较不同蛋白质的局部结构是一种必要的手段。因此,在PACADE系统中增加了搜索类似结构的功能。本文描述了对相同拓扑结构和三维相似拓扑结构的搜索结果。PACADE的用户可以通过改变参数来选择这两种相似度。该功能使推理系统能够根据用户定义的变量约束检索相似的结构。该方法可以自动搜索蛋白质间相似的超二级结构,为蛋白质结构分析提供参考。检索到的相似超二级结构可以作为蛋白质空间定位的标准。
Application of a deductive database system to search for topological and similar three-dimensional structures in protein.
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.