An improved clique-based method for discovery of novel spatial motifs in protein structures

Abstract:
The ability to discover recurring spatial motifs in protein structures will benefit research activities and applications in many fields. In contrast to sequence motifs, discovering spatial motifs are computationally and analytically more difficult due to the added dimensions. This paper presents an improved clique-based method that can quickly discover functionally important structural motifs using graph models of proteins. The method achieves improved speed through exploiting the fact that functionally important residues had the higher evolutionary conservation and the higher degree of structural connectivity. The efficacy of the method was demonstrated by applying it to discover the catalytic triad motif on a set of protein structures. The results showed that the method could discover the catalytic triad motif with an improved speed, and at the same time the method reported a much fewer number of biologically insignificant cliques, which allowed for a recursive approach to precisely discover functionally important spatial motifs shared by a group of proteinstructures.