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.

We have developed a deductive database system PACADE for analyzing 3-D and secondary structures of protein. The PACADE system consists of a relational database created from Protein Data Bank and a deductive engine DEE based on logic programming. It has the following features: (1) The system has an inference mechanism. This means by which users can easily write and check biological hypotheses using logical and declarative rules instead of procedural programs. (2) The relational database of the PACADE system stores data on both 3-D and secondary structures of protein. The integration of this two level structure makes feasible an abstract representation of the protein structure. We describe herein the design, functions, and implementation of this PACADE system.