Entire motifs search of secondary structures in proteins: a parallelization strategy.

The study of proteins is a crucial aspect of the biological field, as they are essential elements of every living cell. Often, the function of a given protein is tightly tied to its geometric structure. Thus, protein structure analysis is an important issue with multiple applications. For example, the ability of a protein to bind other proteins or ligands and the estimation of evolutionary distances between families of proteins are both based on their spatial structure. A key part in the geometric description of a protein is played by the structural motif, a 3D element which appears in a variety of molecules and it is usually made of just a few structures. In this paper we will consider only motifs of secondary structures (SS in the following). The goal is to implement a parallel method to detect the presence and location of all motifs of SSs in a given protein or in a set of proteins. The paper discusses all possible forms of available parallelism, both shared memory and message passing. The analysis is based on existing approaches, such as Secondary Structure Co-Occurrences (SSC) [4, 5] and the Secondary Structure Triplets (SST) [6], both based on the General Hough Transform (GHT) technique [1]. The key idea is to ignore the biological significance on the motifs as much as possible, and to focus on the geometric description of the structures which could be simply viewed as vectors in a 3D space. The paper analyzes a parallel implementation, based on OpenMP. It also hints to a possible exploitation of a hybrid MPI/OpenMP paradigm, useful in the special case of cross protein analysis.