Protein function is expressed by binding to other compounds at a local portion, called an interaction site. Since the structure of its interaction site and function of a protein are closely related, retrieving similar interaction protein is effective in clarifying the function of a protein. We have proposed a method for retrieving similar interaction protein using profiles that represent the features of the interaction site binding to a certain compound. In this method, it is necessary to compare the structure between proteins and a profile, we use geometric hashing technique which is one of the popular methods for structure comparison. However, the problem of structure comparison by using the geometric hashing is that memory usage becomes too large.

This paper proposes a method for arranging the geometric hashing to alleviate this problem. Firstly, only small parts of the target structures are stored in the hash table to reduce the size of the hash table. By evaluating this hash table we screen out candidates of similar structures between target proteins and query profiles. Secondly overall structures are compared for these candidates. In order to reduce the time for retrieval we evaluate the information of the origin which is not generally evaluated without increasing the size of the hash table. Reference Set, the basis for transforming in geometric hashing, are sorted.