Literature DB >> 16258830

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

Sander B Nabuurs1, Elmar Krieger, Chris A E M Spronk, Aart J Nederveen, Gert Vriend, Geerten W Vuister.   

Abstract

For biomolecular NMR structures typically only a poor correspondence is observed between statistics derived from the experimental input data and structural quality indicators obtained from the structure ensembles. Here, we investigate the relationship between the amount of available NMR data and structure quality. By generating datasets with a predetermined information content and evaluating the quality of the resulting structure ensembles we show that there is, in contrast to previous findings, a linear relation between the information contained in experimental data and structural quality. From this relation, a new quality parameter is derived that provides direct insight, on a per-residue basis, into the extent to which structural quality is governed by the experimental input data.

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Year:  2005        PMID: 16258830     DOI: 10.1007/s10858-005-2826-5

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  38 in total

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Journal:  J Biomol NMR       Date:  2003-06       Impact factor: 2.835

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Authors:  N Tjandra; D S Garrett; A M Gronenborn; A Bax; G M Clore
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5.  Phi/psi-chology: Ramachandran revisited.

Authors:  G J Kleywegt; T A Jones
Journal:  Structure       Date:  1996-12-15       Impact factor: 5.006

6.  Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR.

Authors:  T Gallagher; P Alexander; P Bryan; G L Gilliland
Journal:  Biochemistry       Date:  1994-04-19       Impact factor: 3.162

7.  Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy.

Authors:  G M Clore; M A Robien; A M Gronenborn
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8.  Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation.

Authors:  A T Brünger; G M Clore; A M Gronenborn; R Saffrich; M Nilges
Journal:  Science       Date:  1993-07-16       Impact factor: 47.728

9.  The impact of direct refinement against three-bond HN-C alpha H coupling constants on protein structure determination by NMR.

Authors:  D S Garrett; J Kuszewski; T J Hancock; P J Lodi; G W Vuister; A M Gronenborn; G M Clore
Journal:  J Magn Reson B       Date:  1994-05

10.  The solution structure and heme binding of the presequence of murine 5-aminolevulinate synthase.

Authors:  B J Goodfellow; J S Dias; G C Ferreira; P Henklein; V Wray; A L Macedo
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  6 in total

1.  Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.

Authors:  Mark Berjanskii; Jianjun Zhou; Yongjie Liang; Guohui Lin; David S Wishart
Journal:  J Biomol NMR       Date:  2012-06-08       Impact factor: 2.835

2.  The war of tools: how can NMR spectroscopists detect errors in their structures?

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Journal:  J Biomol NMR       Date:  2008-03-05       Impact factor: 2.835

3.  High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.

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Journal:  J Biomol NMR       Date:  2016-12-29       Impact factor: 2.835

4.  A practical implicit solvent potential for NMR structure calculation.

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Review 5.  An overview of tools for the validation of protein NMR structures.

Authors:  Geerten W Vuister; Rasmus H Fogh; Pieter M S Hendrickx; Jurgen F Doreleijers; Aleksandras Gutmanas
Journal:  J Biomol NMR       Date:  2013-07-23       Impact factor: 2.835

6.  CING: an integrated residue-based structure validation program suite.

Authors:  Jurgen F Doreleijers; Alan W Sousa da Silva; Elmar Krieger; Sander B Nabuurs; Christian A E M Spronk; Tim J Stevens; Wim F Vranken; Gert Vriend; Geerten W Vuister
Journal:  J Biomol NMR       Date:  2012-09-18       Impact factor: 2.835

  6 in total

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