title: A minima hopping study of all-atom protein folding and structure prediction.
abstract: The minima hopping algorithm (MHOP) to find global minima on potential energy surfaces is used for protein structure prediction. The energy surface of the protein is represented with an all-atom OPLS force field and an implicit free energy solvation term. The system we studied here is the small 10-residue beta-hairpin mini-protein, chignolin. Starting from a completely extended structure, we found minima with <0.5 A rms coordinate deviation from the geometry-optimized native experimental conformation. A few lowest-energy conformations were used for the calculation of NMR-restraint violations and chemical shifts, and the local minima found during each run leading to the global minimum were connected to trace out a search pathway of the folding process.
authors.affiliation: Departement Physik, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland.
authors.forename: Shantanu
authors.initials: S
authors.lastname: Roy
authors.forename: Stefan
authors.initials: S
authors.lastname: Goedecker
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Field
authors.forename: Evgeni
authors.initials: E
authors.lastname: Penev
mesh_terms: D000465:Algorithms; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins