title: A parallel systematic-Monte Carlo algorithm for exploring conformational space.
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.
authors.affiliation: Department of Proteomics and Bioinformatics, Center for Genetic Engineering and Biotechnology, Havana, Cuba. yasset.perez@biocomp.cigb.edu.cu
authors.forename: Yasset
authors.initials: Y
authors.lastname: Perez-Riverol
authors.forename: Roberto
authors.initials: R
authors.lastname: Vera
authors.forename: Yuliet
authors.initials: Y
authors.lastname: Mazola
authors.forename: Alexis
authors.initials: A
authors.lastname: Musacchio
mesh_terms: D000465:Algorithms; D008968:Molecular Conformation; D009010:Monte Carlo Method