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A minima hopping study of all-atom protein folding and structure prediction
JournalArticle (Originalarbeit in einer wissenschaftlichen Zeitschrift)
 
ID 96578
Author(s) Roy, Shantanu; Goedecker, Stefan; Field, Martin J; Penev, Evgeni
Author(s) at UniBasel Goedecker, Stefan
Year 2009
Title A minima hopping study of all-atom protein folding and structure prediction
Journal The journal of physical chemistry B
Volume 113
Number 20
Pages / Article-Number 7315-7321
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.

Publisher American Chemical Society
ISSN/ISBN 1089-5647
edoc-URL http://edoc.unibas.ch/dok/A5251775
Full Text on edoc No
Digital Object Identifier DOI 10.1021/jp8106793
PubMed ID http://www.ncbi.nlm.nih.gov/pubmed/19391598
ISI-Number WOS:000266093700036
Document type (ISI) Journal Article
 
   

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26/04/2024