Similar Structure Search in a Deductive Database

We developed a deductive database system PACADE (Protein Coordinate Analyzer with Deductive Engine) for analyzing three dimensional and secondary structures of protein. This system has an inference system and a relational database which stores the primary, secondary and tertiary structures converted from Brookhaven's Protein Data Bank (PDB). Users of PACADE can represent biological knowledge on structures of protein in a logical and declarative form and can e ciently search for some iterative structures. However, for protein structure analysis, any function that can only search for structures described by users is not enough and the function to search for similar structures is needed. We describe herein a function to search for similar structure in proteins. Using this function, similar structures can be searched for without calculating the inter-atomic root mean square distance. The outline of the function and some results of searches for super-secondary structure, using the function are given herein, in detail.