Search of protein structural blocks through secondary structure triplets

Abstract

This paper presents an approach for protein motif retrieval founded on protein secondary structures (SSs) in 3D. This is a new way to analyze the protein 3D structure. In this approach, based on the Generalized Hough Transform (GHT), the primitives are the triangles defined by the midpoints of three SSs. The three distances between each SSs couple are used in searching and in the voting process. The barycenter of the motif is assigned as the Reference Point (RP). All motif triangles are compared with all possible triangles in the macromolecule. The lengths of triangle edges are used as selective parameters. For every correspondence a vote is given to the point which is figured out as motif barycenter with a special mapping rule and the point having most votes is determined as candidate RP. In this paper we made some experiments for retrieval of four- and five-SSs motif from the macromolecule. Experimental results showed that the RP is determined with precision and this new approach to retrieve the motif is simple to implement, computationally efficient and fast.