Protein Secondary Structure Detection Using Dihedral Angle Parameters Evaluation

Abstract

The detection of proteins secondary structures constitutes an essential task in the protein motion simulation. Secondary structures constitute rigid parts of the protein structure, hence, their detection is crucial so as to properly define the movement of the protein. During the simulation process, these rigid structures can be identified and, accordingly, their associated degrees of freedom are neglected. As a consequence, the computational cost is reduced. Current methods existing in the literature are based on the analysis of geometrical parameters distribution, such as $C\alpha$ atoms distribution, and hydrogen bonds detection. These methods require specific procedures, independent of the simulation process, to determine these geometrical parameters, thereby increasing the computational cost. In this paper, a novel method for protein secondary structure detection is presented. This new method relies only on the evaluation of dihedral angles so as to detect the existence of secondary structures. The use of dihedral angles, which have been already evaluated during the simulation process, does not increase the computational cost of the simulation process.