Literature DB >> 14505424

Quantitative evaluation of experimental NMR restraints.

Sander B Nabuurs1, Chris A E M Spronk, Elmar Krieger, Hans Maassen, Gert Vriend, Geerten W Vuister.   

Abstract

Nuclear Overhauser effect (NOE) data are an indispensable source of structural information in biomolecular structure determination by NMR spectroscopy. The number and type of experimental restraints used in the structure calculation and the RMS deviation of the restraints are usually reported. We present a new method for quantifying the information contained in the experimental NMR restraints. The method is based on a description of the structure in distance space and concepts derived from information theory. It allows for an objective description of the amount of available experimental information, which we show to be related to the positional uncertainty of the NMR ensemble. The measure of information presented is not affected by redundancy in the experimental restraints. Using various examples, we show that the method successfully identifies the crucial restraints in a structure determination: those restraints that are both important and unique. Finally, we demonstrate that the method can detect a wider range of redundancy in experimental datasets when compared to currently available methods. Because our method describes the quantitative evaluation of experimental NMR restraints, we propose the acronym QUEEN.

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Year:  2003        PMID: 14505424     DOI: 10.1021/ja035440f

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  29 in total

1.  Definition of a new information-based per-residue quality parameter.

Authors:  Sander B Nabuurs; Elmar Krieger; Chris A E M Spronk; Aart J Nederveen; Gert Vriend; Geerten W Vuister
Journal:  J Biomol NMR       Date:  2005-10       Impact factor: 2.835

2.  Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.

Authors:  N Powers; Jan H Jensen
Journal:  J Biomol NMR       Date:  2006-06-03       Impact factor: 2.835

3.  KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies.

Authors:  Naohiro Kobayashi; Junji Iwahara; Seizo Koshiba; Tadashi Tomizawa; Naoya Tochio; Peter Güntert; Takanori Kigawa; Shigeyuki Yokoyama
Journal:  J Biomol NMR       Date:  2007-07-18       Impact factor: 2.835

4.  Solution structure of the factor H-binding protein, a survival factor and protective antigen of Neisseria meningitidis.

Authors:  Francesca Cantini; Daniele Veggi; Sara Dragonetti; Silvana Savino; Maria Scarselli; Giacomo Romagnoli; Mariagrazia Pizza; Lucia Banci; Rino Rappuoli
Journal:  J Biol Chem       Date:  2009-02-04       Impact factor: 5.157

5.  A robust method for quantitative identification of ordered cores in an ensemble of biomolecular structures by non-linear multi-dimensional scaling using inter-atomic distance variance matrix.

Authors:  Naohiro Kobayashi
Journal:  J Biomol NMR       Date:  2014-01-03       Impact factor: 2.835

6.  Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions.

Authors:  Lee-Wei Yang; Eran Eyal; Chakra Chennubhotla; JunGoo Jee; Angela M Gronenborn; Ivet Bahar
Journal:  Structure       Date:  2007-06       Impact factor: 5.006

7.  Targeted 13C-13C distance measurements in a microcrystalline protein via J-decoupled rotational resonance width measurements.

Authors:  Patrick C A van der Wel; Matthew T Eddy; Ramesh Ramachandran; Robert G Griffin
Journal:  Chemphyschem       Date:  2009-07-13       Impact factor: 3.102

8.  Recommendations of the wwPDB NMR Validation Task Force.

Authors:  Gaetano T Montelione; Michael Nilges; Ad Bax; Peter Güntert; Torsten Herrmann; Jane S Richardson; Charles D Schwieters; Wim F Vranken; Geerten W Vuister; David S Wishart; Helen M Berman; Gerard J Kleywegt; John L Markley
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

9.  Spinning-rate encoded chemical shift correlations from rotational resonance solid-state NMR experiments.

Authors:  Jun Li; Patrick C A van der Wel
Journal:  J Magn Reson       Date:  2013-02-14       Impact factor: 2.229

10.  X-ray vs. NMR structures as templates for computational protein design.

Authors:  Michael Schneider; Xiaoran Fu; Amy E Keating
Journal:  Proteins       Date:  2009-10
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