Related ArticlesAn assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors.
J Mol Biol. 1994 Jun 24;239(5):601-7
Authors: Zhao D, Jardetzky O
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.
[KPWU blog] statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)
statistics of NMR/X-ray determined protein structures in PDB (up to May 10, 2011)
Two brief plots of protein structures (protein-DNA/RNA/ligand complexes are excluded) determined by either X-ray or NMR. Structures determined by hybrid method are not counted in the two plots. The dataset was obtain from PDB based on its released statistics by May 10th, 2011. Molecules with sequence length longer than 1200 residues are also excluded. There http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=380&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
nmrlearner
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05-17-2011 08:30 AM
[NMR paper] Assessing precision and accuracy of protein structures derived from NMR data.
Assessing precision and accuracy of protein structures derived from NMR data.
Related Articles Assessing precision and accuracy of protein structures derived from NMR data.
Proteins. 2005 Jun 1;59(4):655-61
Authors: Snyder DA, Bhattacharya A, Huang YJ, Montelione GT
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11-25-2010 08:21 PM
[NMR paper] Influence of internal dynamics on accuracy of protein NMR structures: derivation of r
Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.
Related Articles Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.
J Mol Biol. 1999 Jan 15;285(2):727-40
Authors: Schneider TR, Brünger AT, Nilges M
In order to study the effect of internal dynamics on the accuracy of NMR structures in detail, we generated NOE distance data from a...
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11-18-2010 07:05 PM
[NMR paper] Accuracy and precision of NMR relaxation experiments and MD simulations for character
Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics.
Proteins. 1997 Aug;28(4):481-93
Authors: Philippopoulos M, Mandel AM, Palmer AG, Lim C
Model-free parameters obtained from nuclear magnetic resonance (NMR) relaxation...
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08-22-2010 05:08 PM
[NMR paper] An assessment of the precision and accuracy of protein structures determined by NMR.
An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors.
J Mol Biol. 1994 Jun 24;239(5):601-7
Authors: Zhao D, Jardetzky O
We tested the dependence of the accuracy and precision of calculated NMR structures on the errors of the distance constraints...
nmrlearner
Journal club
0
08-22-2010 03:33 AM
[NMR paper] Defining the precision with which a protein structure is determined by NMR. Applicati
Defining the precision with which a protein structure is determined by NMR. Application to motilin.
Related Articles Defining the precision with which a protein structure is determined by NMR. Application to motilin.
Biochemistry. 1993 Feb 16;32(6):1610-7
Authors: Shriver J, Edmondson S
A simple procedure is introduced for accurately defining the precision with which the Cartesian coordinates of any macromolecular structure are determined by nuclear Overhauser data. The method utilizes an ensemble of structures obtained from an array of...
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08-21-2010 11:53 PM
Precision and Accuracy of NMR Structures - PSI
Precision and Accuracy of NMR Structures - a presentation by the Protein Structure Initiative - is available to read from here:
http://journals.iucr.org/services/nmr/precision.pdf
More information about the PSI can be found here:
http://www.structuralgenomics.org/
Rachel
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09-10-2008 05:32 PM
Assessing precision and accuracy of protein struct
Editor's Corner
Assessing precision and accuracy of protein structures derived from NMR data
David A. Snyder 1 2, Aneerban Bhattacharya 1 2, Yuanpeng J. Huang 1 2, Gaetano T. Montelione 1 2 *
1Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers University, Piscataway, NJ 08854
2Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ 08854
*Correspondence to Gaetano T. Montelione, CABM-Rutgers University, 679 Hoes Lane, Piscataway, NJ...
An assessment of the precision and accuracy of protein structures determined by NMR.
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