Abstract
Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11*% of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate proper analysis of the experimental models, a number of program suites are available. We discuss nine of these tools in this review: PROCHECK-NMR, PSVS, GLM-RMSD, CING, Molprobity, Vivaldi, ResProx, NMR constraints analyzer and QMEAN. We evaluate these programs for their ability to assess the structural quality, restraints and their violations, chemical shifts, peaks and the handling of multi-model NMR ensembles. We document both the input required by the programs and output they generate. To discuss their relative merits we have applied the tools to two representative examples from the PDB: a small, globular monomeric protein (Staphylococcal nuclease from S. aureus, PDB entry 2kq3) and a small, symmetric homodimeric protein (a region of human myosin-X, PDB entry 2lw9).
PMID: 23877928 [PubMed - as supplied by publisher]
[NMR paper] CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data.
J Comput Chem. 2013 Jul 6;
Authors: Huang J, Mackerell AD
Abstract
Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR...
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07-09-2013 02:47 PM
Overview on the use of NMR to examine protein structure.
Overview on the use of NMR to examine protein structure.
Overview on the use of NMR to examine protein structure.
Curr Protoc Protein Sci. 2011 Apr;Chapter 17:Unit17.5
Authors: Breukels V, Konijnenberg A, Nabuurs SM, Doreleijers JF, Kovalevskaya NV, Vuister GW
Any protein structure determination process contains several steps, starting from obtaining a suitable sample, then moving on to acquiring data and spectral assignment, and lastly to the final steps of structure determination and validation. This unit describes all of these steps, starting...
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04-14-2011 10:04 AM
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures.
Proteins. 2011 Jan 6;
Authors: Bernard A, Vranken WF, Bardiaux B, Nilges M, Malliavin TE
The classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal...
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03-03-2011 12:34 PM
[NMR paper] Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Related Articles Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Proteins. 2005 Jul 1;60(1):139-47
Authors: Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV
We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures...
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12-01-2010 06:56 PM
[NMR paper] Rapid assessment of protein structural stability and fold validation via NMR.
Rapid assessment of protein structural stability and fold validation via NMR.
Related Articles Rapid assessment of protein structural stability and fold validation via NMR.
Methods Enzymol. 2005;394:142-75
Authors: Hoffmann B, Eichmüller C, Steinhauser O, Konrat R
In structural proteomics, it is necessary to efficiently screen in a high-throughput manner for the presence of stable structures in proteins that can be subjected to subsequent structure determination by X-ray or NMR spectroscopy. Here we illustrate that the (1)H chemical...
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11-24-2010 11:14 PM
[NMR paper] Tools for the automated assignment of high-resolution three-dimensional protein NMR s
Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques.
Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques.
J Biomol NMR. 1997 Oct;10(3):207-19
Authors: Croft D, Kemmink J, Neidig KP, Oschkinat H
One of the major bottlenecks in the determination of proteinstructures by NMR is in the evaluation of the data produced by theexperiments. An important step in this process is assignment, where...
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08-22-2010 05:08 PM
Validation of NMR-derived protein structures, Chris Spronk
Here's a good PowerPoint presentation by Chris Spronk (University of Nijmegen, The Netherlands) on the subject of validating NMR protein structure results (adapted by Jurgen F. Doreleijers - University of Wisconsin, Madison, USA)
http://tang.bmrb.wisc.edu/~jurgen/presents/Madison/Biochem%20801/NMR_validation_biochem801_2005.ppt
The presentation is very well-annotated, so be sure to adjust your view in PowerPoint so that you can see the notes.
jen
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09-02-2008 05:37 PM
The war of tools: how can NMR spectroscopists detect errors in their structures?
The war of tools: how can NMR spectroscopists detect errors in their structures?
Edoardo Saccenti and Antonio Rosato
Journal of Biomolecular NMR; 2008; 40(4) pp 251 - 261
Abstract:
Protein structure determination by NMR methods has started in the mid-eighties and has been growing steadily since then. Ca. 14% of the protein structures deposited in the PDB have been solved by NMR. The evaluation of the quality of NMR structures however is still lacking a well-established practice. In this work, we examined various tools for the assessment of structural quality to ascertain the extent to...
An overview of tools for the validation of protein NMR structures.
Linear Mode
