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2012 ; 4
(3
): 189-203
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Assessing and refining molecular dynamics simulations of proteins with nuclear
magnetic resonance data
#MMPMID28510078
Allison JR
Biophys Rev
2012[Sep]; 4
(3
): 189-203
PMID28510078
show ga
The sophistication of the force fields, algorithms and hardware used for
molecular dynamics (MD) simulations of proteins is continuously increasing. No
matter how advanced the methodology, however, it is essential to evaluate the
appropriateness of the structures sampled in a simulation by comparison with
quantitative experimental data. Solution nuclear magnetic resonance (NMR) data
are particularly useful for checking the quality of protein simulations, as they
provide both structural and dynamic information on a variety of temporal and
spatial scales. Here, various features and implications of using NMR data to
validate and bias MD simulations are outlined, including an overview of the
different types of NMR data that report directly on structural properties and of
relevant simulation techniques. The focus throughout is on how to properly
account for conformational averaging, particularly within the context of the
assumptions inherent in the relationships that link NMR data to structural
properties.