Related ArticlesA method for validating the accuracy of NMR protein structures.
Nat Commun. 2020 Dec 18;11(1):6321
Authors: Fowler NJ, Sljoka A, Williamson MP
Abstract
We present a method that measures the accuracy of NMR protein structures. It compares random coil index [RCI] against local rigidity predicted by mathematical rigidity theory, calculated from NMR structures [FIRST], using a correlation score (which assesses secondary structure), and an RMSD score (which measures overall rigidity). We test its performance using: structures refined in explicit solvent, which are much better than unrefined structures; decoy structures generated for 89 NMR structures; and*conventional predictors of accuracy such as number of restraints per residue, restraint violations, energy of structure, ensemble RMSD, Ramachandran distribution, and clashscore. Restraint violations and RMSD are poor measures of accuracy. Comparisons of NMR to crystal structures show that secondary structure is equally accurate, but crystal structures are typically too rigid in loops, whereas NMR structures are typically too floppy overall. We show that the method is a useful addition to existing measures of accuracy.
[NMR paper] High accuracy protein structures from minimal sparse paramagnetic solid-state NMR restraints.
High accuracy protein structures from minimal sparse paramagnetic solid-state NMR restraints.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7315-19-Wiley_FullText_120x30_orange.png Related Articles High accuracy protein structures from minimal sparse paramagnetic solid-state NMR restraints.
Angew Chem Int Ed Engl. 2019 Mar 26;:
Authors: Perez A, Gaalswyk K, Jaroniec CP, MacCallum JL
Abstract
There is a pressing need for new computational tools to integrate data from diverse...
Validating hits through NMR as an orthogonal biophysical method - News-Medical.net
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Validating hits through NMR as an orthogonal biophysical method
News-Medical.net
It can therefore be complemented with the use of Nuclear Magnetic Resonance (NMR), an orthogonal biophysical method that can detect target-ligand interactions with high sensitivity but that necessitates a high consumption of protein compared to other ...
Validating hits through NMR as an orthogonal biophysical method -...
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[NMR paper] Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
J Am Chem Soc. 2014 Jan 6;
Authors: Mao B, Tejero R, Baker D, Montelione GT
Abstract
We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement...
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01-08-2014 11:23 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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[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...
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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...
A method for validating the accuracy of NMR protein structures.
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