title: An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides.
abstract: Replica exchange molecular dynamics simulations were performed to test the ability of six AMBER force fields and three implicit solvent models of predicting the native conformation of two helical peptides, three β-hairpins, and three intrinsically disordered peptides. Although a combination of the force field and implicit solvation models able to accurately predict the native structure of all the considered peptides was not identified, we found that the GB-Neck2 model seems to well compensate for some of the conformational biases showed by ff96 and ff99SB/ildn/ildn-φ. Indeed, the force fields of the ff99SB series coupled with GB-Neck2 reasonably discriminated helices from disordered peptides, while a good prediction of β-hairpin conformations was only achieved by performing two independent simulations: one with the ff96/GB-Neck2 combination and the other with GB-Neck2 coupled with any of the ff99SB/ildn/ildn-φ force fields.
authors.affiliation: Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy.
authors.forename: Irene
authors.initials: I
authors.lastname: Maffucci
authors.affiliation: Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Contini
mesh_terms: D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D010455:Peptides; D012997:Solvents