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Accurate NMR Structures Through Minimization of an Extended Hybrid Energy

Authors :
Michael Nilges
Michael Habeck
Wolfgang Rieping
Thérèse E. Malliavin
Aymeric Bernard
Benjamin Bardiaux
Bioinformatique Structurale
Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Max Planck Institute for Developmental Biology
Max-Planck-Gesellschaft
Max Planck Institute for Biological Cybernetics
University of Cambridge [UK] (CAM)
This work was funded by EC grants QLG2-CT-2000-01313 and QLG2–CT– 2002–00988 (to M.N.) and the ACI IMPBio ICMD-RMN (to T.M.
European Project: QLG2-CT-2002-00988,SPINE(2002)
Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Source :
Structure, Structure, 2008, 16 (9), pp.1305-12. ⟨10.1016/j.str.2008.07.008⟩, Structure, Elsevier (Cell Press), 2008, 16 (9), pp.1305-12. ⟨10.1016/j.str.2008.07.008⟩
Publication Year :
2008
Publisher :
Elsevier BV, 2008.

Abstract

International audience; 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.

Details

ISSN :
09692126
Volume :
16
Database :
OpenAIRE
Journal :
Structure
Accession number :
edsair.doi.dedup.....754aff0d8bdbb8c13913d90428e7221e