Accurate NMR structures through minimization of an extended hybrid energy.
The use of generous distance bounds has been the hallmark of NMR structure determination. However, bounds necessitate the estimation of data quality before the calculation, reduce the information content, introduce human bias, and allow for major errors in the structures. Here, we propose a new rapid structure calculation scheme based on Bayesian analysis. The minimization of an extended energy function, including a new type of distance restraint and a term depending on the data quality, results in an estimation of the data quality in addition to coordinates. This allows for the determination of the optimal weight on the experimental information. The resulting structures are of better quality and closer to the X-ray crystal structure of the same molecule. With the new calculation approach, the analysis of discrepancies from the target distances becomes meaningful. The strategy may be useful in other applications-for example, in homology modeling.
Nilges
Michael
M
Institut Pasteur, Département de Biologie Structurale et Chimie, Unité de Bio-informatique Structurale, CNRS URA 2185, 25-28 rue du docteur Roux, F-75015 Paris, France. nilges@pasteur.fr
Bernard
Aymeric
A
Bardiaux
Benjamin
B
Malliavin
Thérèse
T
Habeck
Michael
M
Rieping
Wolfgang
W
D000465:Algorithms; D018360:Crystallography, X-Ray; D004735:Energy Transfer / Q000502:physiology*; D006801:Humans; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D008970:Molecular Weight; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D012680:Sensitivity and Specificity