Abstract
Biomolecular NMR structures are now routinely used in biology, chemistry, and bioinformatics. Methods and metrics for assessing the accuracy and precision of protein NMR structures are beginning to be standardized across the biological NMR community. These include both knowledge-based assessment metrics, parameterized from the database of protein structures, and model versus data assessment metrics. On line servers are available that provide comprehensive protein structure quality assessment reports, and efforts are in progress by the world-wide Protein Data Bank (wwPDB) to develop a biomolecular NMR structure quality assessment pipeline as part of the structure deposition process. These quality assessment metrics and standards will aid NMR spectroscopists in determining more accurate structures, and increase the value and utility of these structures for the broad scientific community.
PMID: 24060334 [PubMed - as supplied by publisher]
Quality assessment of protein NMR structures
Quality assessment of protein NMR structures
Publication date: Available online 21 September 2013
Source:Current Opinion in Structural Biology</br>
Author(s): Antonio Rosato , Roberto Tejero , Gaetano T Montelione</br>
Biomolecular NMR structures are now routinely used in biology, chemistry, and bioinformatics. Methods and metrics for assessing the accuracy and precision of protein NMR structures are beginning to be standardized across the biological NMR community. These include both knowledge-based assessment metrics, parameterized from the database of protein...
nmrlearner
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09-21-2013 06:50 PM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
January 2012
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction...
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12-15-2012 09:51 AM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
January 2012
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction...
nmrlearner
Journal club
0
12-01-2012 06:10 PM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Publication year: 2012
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 60</br>
Jakob T. Nielsen, Hamid R. Eghbalnia, Niels Chr. Nielsen</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise,...
nmrlearner
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03-09-2012 09:16 AM
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
Publication year: 2011
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 23 May 2011</br>
Jakob T., Nielsen , Hamid R., Eghbalnia , Niels Chr., Nielsen</br>
The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we...
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05-24-2011 10:02 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.
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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
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08-22-2010 03:33 AM
[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 RPF: new NMR quality assessment scores
Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.
Huang YJ, Powers R, Montelione GT.
Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers University, Northeast Structural Genomics Consortium, and Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5368, USA.
J Am Chem Soc. 2005 Feb 16;127(6):1665-74.
Abstract: