Discovering Functional Sites of Amino Acid Sequences Using Sorted Variable Generalization

Abstract

This research develops a method for discovering functional sites of amino acid sequences using an Inductive Logic Programming (ILP) method with sorted variable generalization. Functional sites provide clues to building a knowledge base for prediction of protein functions from amino acid sequences. The proposed method generates hypotheses of functional sites directly from aligned amino acid sequences using an ILP method extended with sorted variable generalization. The proposed method is shown to be useful for discovering functional sites by an example application to the case of bacteriorhodopsin-like proteins.