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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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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 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
Bibsysno:Link to catalogue
Publisher:American Chemical Society
ISSN:1089-5647
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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