A Parallel Systematic-Monte Carlo Algorithm for Exploring Conformational Space

Yasset      Perez-Riverol; Roberto      Vera; Yuliet      Mazola; Alexis      Musacchio

doi:10.2174/1568026611209061790

Abstract

Computational algorithms to explore the conformational space of small molecules are complex and computer demand field in chemoinformatics. In this paper a hybrid algorithm to explore the conformational space of organic molecules is presented. This hybrid algorithm is based in a systematic search approach combined with a Monte Carlo based method in order to obtain an ensemble of low-energy conformations simulating the flexibility of small chemical compounds. The Monte Carlo method uses the Metropolis criterion to accept or reject a conformation through an in-house implementation of the MMFF94s force field to calculate the conformational energy. The parallel design of this algorithm, based on the message passing interface (MPI) paradigm, was implemented. The results showed a performance increase in the terms of speed and efficiency.

Keywords: Parallel programming, chemoinformatics, conformational search, molecular docking, virtual screening, Monte Carlo based method, message passing interface (MPI) paradigm, efficiency