APPLICATION OF A DEDUCTIVE DATABASE SYSTEM TO SEARCH FOR TOPOLOGICAL AND SIMILAR 3-DIMENSIONAL STRUCTURES IN PROTEIN

A deductive database system FACADE (Protein Atomic Coordinate Analyzer with Deductive Engine) has been developed for protein structure analy sis. With this system, super-secondary structures described in logical and declarative rules can be retrieved effectively. For protein struc ture analysis comparison of local structures in different proteins is a necessary mean. A function to search for similar structures has, the refore, been added to the PACADE system. We describe herein the result of searches for the same topological structures and three-dimensional ly similar ones. A user of PACADE can select these two levels of simil arity by changing parameters. This function enables the inference syst em to retrieve similar structure, according to the restraints of varia bles defined by the user. Similar super-secondary structures among pro teins can be searched for automatically, which is useful for protein s tructure analysis. The retrieved similar super-secondary structures ca n serve as criteria for protein spatial alignment.