title: Systematic validation of protein force fields against experimental data.
abstract: Molecular dynamics simulations provide a vehicle for capturing the structures, motions, and interactions of biological macromolecules in full atomic detail. The accuracy of such simulations, however, is critically dependent on the force field--the mathematical model used to approximate the atomic-level forces acting on the simulated molecular system. Here we present a systematic and extensive evaluation of eight different protein force fields based on comparisons of experimental data with molecular dynamics simulations that reach a previously inaccessible timescale. First, through extensive comparisons with experimental NMR data, we examined the force fields' abilities to describe the structure and fluctuations of folded proteins. Second, we quantified potential biases towards different secondary structure types by comparing experimental and simulation data for small peptides that preferentially populate either helical or sheet-like structures. Third, we tested the force fields' abilities to fold two small proteins--one α-helical, the other with β-sheet structure. The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins.
authors.affiliation: DE Shaw Research, New York, New York, United States of America.
authors.forename: Kresten
authors.initials: K
authors.lastname: Lindorff-Larsen
authors.forename: Paul
authors.initials: P
authors.lastname: Maragakis
authors.forename: Stefano
authors.initials: S
authors.lastname: Piana
authors.forename: Michael P
authors.initials: MP
authors.lastname: Eastwood
authors.forename: Ron O
authors.initials: RO
authors.lastname: Dror
authors.forename: David E
authors.initials: DE
authors.lastname: Shaw
mesh_terms: D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D006801:Humans; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D025801:Ubiquitin / Q000737:chemistry
chemical_list: D010455:Peptides; D011506:Proteins; D025801:Ubiquitin