A minima hopping study of all-atom protein folding and structure prediction

Roy, Shantanu and Goedecker, Stefan and Field, Martin J. and Penev, Evgeni. (2009) A minima hopping study of all-atom protein folding and structure prediction. The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical chemistry, Vol. 113, No. 20. pp. 7315-7321.

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Official URL: http://edoc.unibas.ch/dok/A5251775

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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 angstrom 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.
Faculties and Departments:05 Faculty of Science > Departement Physik > Physik > Physik (Goedecker)
UniBasel Contributors:Goedecker, Stefan
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:American Chemical Society
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:22 Mar 2012 14:23
Deposited On:22 Mar 2012 13:34

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