Similarity search for protein structures by sonification.

Abstract

Comparison of protein structures is important to understand and predict their functions. The protein structure is complicated, so comparing is not straightforward. In general, the similarity is evaluated by amino acid sequence analyzed by the homology search. In this study, we develop a method that evaluates similarity of protein structure reflecting interactions with surrounding amino acids. For easy comparison of protein structures, we propose a method of sonification which expresses three-dimensional structural features. In the method, surrounding amino acids for one target amino acid are expressed as overlap of sounds generated from each amino acid. In the overall sound, the distance information is taken into account in the sonification. By this method, we can quantitatively evaluate similarity/difference of 3D protein structures in a data in a lower dimension.