Energy minimizations with a combination of two knowledge-based potentials for protein folding.
New force fields that are both simple and accurate are needed for computationally efficient molecular simulation studies to give insight into the actual features of the protein folding process. In this work, we assess a force field based on a new combination of two coarse-grained potentials taken from the bibliography. These potentials have already been proved efficient in representing different types of interactions, namely the side-chain interactions and the backbone hydrogen bonds. Now we combine them weighing their contribution to the global energy with a very simplified parameterization. To assess this combination of potentials, we use our evolutionary method to carry out energy minimization experiments for a set of all-alpha, all-beta, and (alpha + beta) protein structures. Our results, based on the assembly of short rigid native fragments, suggest that this combination of potentials can be successfully employed in coarse-grained folding simulations.
de Sancho
David
D
Departamento de Quĩmica Fĩsica I, Universidad Complutense, Madrid, Spain.
Rey
Antonio
A
D000465:Algorithms; D006860:Hydrogen Bonding; D008956:Models, Chemical; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins