title: Assessing the Quality of the OPEP Coarse-Grained Force Field.
abstract: A coarse-grained potential that could accurately describe the overall conformational landscape of proteins would be extremely valuable not only for structure prediction but also for studying protein dynamics, large conformational motions, and intrinsically disordered systems. Here, we assessed the quality of the OPEP coarse-grained potential by comparing the reconstructed free-energy surfaces (FESs) of two prototypical β-hairpin and α-helix peptides to all-atom calculations in explicit solvent. We found remarkable agreement between the OPEP FES and those obtained using atomistic models, despite a general overstabilization of α- and β-structures by the coarse-grained potential. The use of advanced sampling techniques based on metadynamics and parallel tempering guaranteed a thorough exploration of the conformational space accessible to the two peptides studied.
authors.affiliation: Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich , c/o USI Campus, via Buffi 13, CH-6900 Lugano, Switzerland.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Barducci
authors.affiliation: Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich , c/o USI Campus, via Buffi 13, CH-6900 Lugano, Switzerland.
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Bonomi
authors.affiliation: Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique and Université Paris Diderot, Paris 7, Institut Universitaire de France , 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Derreumaux