Genetic algorithms coupled with quantum mechanics for refinement of force fields for RNA simulation: a case study of glycosidic torsions in the canonical ribonucleosides

Abstract

We report the use of genetic algorithms (GA) as a method to refine force field parameters in order to determine RNA energy. Quantum-mechanical (QM) calculations are carried out for the isolated canonical ribonucleosides (adenosine, guanosine, cytidine and uridine) that are taken as reference data. In this particular study, the dihedral and electrostatic energies are reparametrized in order to test the proposed approach, i.e., GA coupled with QM calculations. Overall, RMSE comparison with recent published results for ribonucleosides energies shows an improvement, on average, of 50%. Finally, the new reparametrized potential energy function is used to determine the spatial structure of RNA (PDB code 1r4h) that was not taken into account in the parametrization process. This structure was improved about 82% comparable with previously published results.