Automatic profile extraction based on frequency distribution of atoms for retrieving similar interaction protein

Abstract

Protein function is closely related to the structure of interaction site of the protein. Proteins that have similar structure at interaction sites often bind to the same compound. 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. Since it takes a long time to extract a profile manually, automatic extraction of a profile from the protein structure data is highly required. This paper presents a method for automatic profile extraction based on frequency distribution of atoms. The profile extracted by using the proposed method was closely similar to the profile extracted manually. Retrieval experiment shows that the accuracy of identifying correct interaction sites using a profile generated by the proposed method is equivalent to the result using a manually constructed profile.