A method of filtering protein surface motifs based on similarity among local surfaces

Abstract

We have developed a system for extracting surface motifs from protein molecular surface database called SUrface MOtif mining MOdule (SUMOMO). However, SUMOMO tends to extract a large amount of surface motifs making it difficult to distinguish whether they are true active sites. Since active sites, from proteins having a particular function, have similar shape and physical properties, proteins can be classified based on similarity among local surfaces. Thus, motifs extracted from proteins from the same group can be considered significant, and rest can be filtered out. The proposed method is applied to 3,183 surface motifs extracted from 15 proteins belonging to each of four function groups. As a result, the number of motifs is reduced to 14.1% without elimination of important motifs that correspond to the four functional sites. © Springer-Verlag Berlin Heidelberg 2004.