Journal of Biomolecular NMR

, Volume 25, Issue 3, pp 225–234 | Cite as

The precision of NMR structure ensembles revisited

  • Chris A.E.M. Spronk
  • Sander B. Nabuurs
  • Alexandre M.J.J. Bonvin
  • Elmar Krieger
  • Geerten W. Vuister
  • Gert Vriend
Article

Abstract

Biomolecular structures provide the basis for many studies in research areas such as structure-based drug design and homology modeling. In order to use molecular coordinates it is important that they are reliable in terms of accurate description of the experimental data and in terms of the overall and local geometry. Besides these primary quality criteria an indication is needed for the uncertainty in the atomic coordinates that may arise from the dynamic behavior of the considered molecules as well as from experimental- and computational procedures.

In contrast to the crystallographic B-factor, a good measure for the uncertainty in NMR-derived atomic coordinates is still not available. It has become clear in recent years that the widely used atomic Root Mean Square Deviation (RMSD), which is a measure for the precision of the data, overestimates the accuracy of NMR structure ensembles and therefore is a problematic measure for the uncertainty in the atomic coordinates.

In this study we report a method that yields a more realistic estimate of the uncertainty in the atomic coordinates by maximizing the RMSD of an ensemble of structures, while maintaining the accordance with the experimentally derived data. The results indicate that the RMSD of most NMR structure ensembles can be significantly increased compromising neither geometric quality nor NMR data. This maximized RMSD therefore seems a better estimate of the true uncertainty in the atomic coordinates.

accuracy NMR structures precision structure refinement structure validation 

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Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Chris A.E.M. Spronk
    • 1
  • Sander B. Nabuurs
    • 1
  • Alexandre M.J.J. Bonvin
    • 2
  • Elmar Krieger
    • 1
  • Geerten W. Vuister
    • 3
  • Gert Vriend
    • 1
  1. 1.Centre for Molecular and Biomolecular InformaticsUniversity of NijmegenThe Netherlands
  2. 2.Department of NMR-spectroscopyUniversity of UtrechtThe Netherlands
  3. 3.Department of Biophysical ChemistryUniversity of NijmegenThe Netherlands

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