Literature DB >> 8014985

An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors.

D Zhao1, O Jardetzky.   

Abstract

We tested the dependence of the accuracy and precision of calculated NMR structures on the errors of the distance constraints using sequential simulated annealing and found that: (1) the accuracy of the family of structures depends mainly on the quality of the data, but is no better than about 1 A even if the errors in distance constraints are smaller than +/- 1 A. (2) The precision of the calculated structures, on the other hand, is nearly insensitive to the quality of the data. With present methods, the accuracy of NMR structures is at best of the order of 1 to 2 A, although a precision of 0.4 to 0.7 A is readily attainable. Comparisons with recent studies of this problem also brought out the importance of distinguishing between correct and incorrect definitions of accuracy when reporting numerical estimates. Using an incorrect definition of the term accuracy can lead to an artificially favorable estimate of its numerical value.

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Year:  1994        PMID: 8014985     DOI: 10.1006/jmbi.1994.1402

Source DB:  PubMed          Journal:  J Mol Biol        ISSN: 0022-2836            Impact factor:   5.469


  23 in total

1.  Variability in automated assignment of NOESY spectra and three-dimensional structure determination: a test case on three small disulfide-bonded proteins.

Authors:  P Savarin; S Zinn-Justin; B Gilquin
Journal:  J Biomol NMR       Date:  2001-01       Impact factor: 2.835

2.  Paramagnetism-based versus classical constraints: an analysis of the solution structure of Ca Ln calbindin D9k.

Authors:  I Bertini; A Donaire; B Jiménez; C Luchinat; G Parigi; M Piccioli; L Poggi
Journal:  J Biomol NMR       Date:  2001-10       Impact factor: 2.835

3.  The precision of NMR structure ensembles revisited.

Authors:  Chris A E M Spronk; Sander B Nabuurs; Alexandre M J J Bonvin; Elmar Krieger; Geerten W Vuister; Gert Vriend
Journal:  J Biomol NMR       Date:  2003-03       Impact factor: 2.835

4.  Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space.

Authors:  Daniel Gottstein; Donata K Kirchner; Peter Güntert
Journal:  J Biomol NMR       Date:  2012-02-22       Impact factor: 2.835

5.  Automated detection of problem restraints in NMR data sets using the FINGAR genetic algorithm method.

Authors:  D A Pearlman
Journal:  J Biomol NMR       Date:  1999-04       Impact factor: 2.835

6.  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

7.  Estimating the accuracy of protein structures using residual dipolar couplings.

Authors:  Katya Simon; Jun Xu; Chinpal Kim; Nikolai R Skrynnikov
Journal:  J Biomol NMR       Date:  2005-10       Impact factor: 2.835

8.  Predicting 13Calpha chemical shifts for validation of protein structures.

Authors:  Jorge A Vila; Myriam E Villegas; Hector A Baldoni; Harold A Scheraga
Journal:  J Biomol NMR       Date:  2007-06-09       Impact factor: 2.835

9.  Use of 13Calpha chemical shifts in protein structure determination.

Authors:  Jorge A Vila; Daniel R Ripoll; Harold A Scheraga
Journal:  J Phys Chem B       Date:  2007-05-22       Impact factor: 2.991

10.  Solution structure of a Lewis(x) analogue by off-resonance 1H NMR spectroscopy without use of an internal distance reference.

Authors:  P Berthault; N Birlirakis; G Rubinstenn; P Sinaÿ; H Desvaux
Journal:  J Biomol NMR       Date:  1996-07       Impact factor: 2.835

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