A DEDUCTIVE DATABASE SYSTEM PACADE FOR ANALYZING 3-D AND SECONDARY STRUCTURES OF PROTEIN

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.