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Physics‐based protein structure refinement through multiple molecular dynamics trajectories and structure averaging
Author(s) -
Mirjalili Vahid,
Noyes Keenan,
Feig Michael
Publication year - 2014
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24336
Subject(s) - molecular dynamics , computer science , protein structure prediction , casp , sampling (signal processing) , protein structure , biological system , statistical physics , algorithm , chemistry , computational chemistry , physics , biology , filter (signal processing) , computer vision , biochemistry
We used molecular dynamics (MD) simulations for structure refinement of Critical Assessment of Techniques for Protein Structure Prediction 10 (CASP10) targets. Refinement was achieved by selecting structures from the MD‐based ensembles followed by structural averaging. The overall performance of this method in CASP10 is described, and specific aspects are analyzed in detail to provide insight into key components. In particular, the use of different restraint types, sampling from multiple short simulations versus a single long simulation, the success of a quality assessment criterion, the application of scoring versus averaging, and the impact of a final refinement step are discussed in detail. Proteins 2014; 82(Suppl 2):196–207. © 2013 Wiley Periodicals, Inc.