Related ArticlesCompleteness of NOEs in protein structure: a statistical analysis of NMR.
J Biomol NMR. 1999 Jun;14(2):123-32
Authors: Doreleijers JF, Raves ML, Rullmann T, Kaptein R
The completeness of experimentally observed NOE restraints of a set of 97 NMR protein structures deposited in the PDB has been assessed. Completeness is defined as the ratio of the number of experimentally observed NOEs and the number of 'expected NOEs'. A practical definition of 'expected NOEs' based on inter-proton distances in the structures up to a given cut-off distance is proposed. The average completeness for the set of 97 structures is 68, 48, and 26% up to 3, 4, and 5 A cut-off distances, respectively. For recent state-of-the-art structures these numbers are approximately 90, 75, and 45%. Almost 20% of the observed NOEs are between atoms that are further than 5 A apart in the final structures. The completeness is independent of the relative surface accessibility and does not depend strongly on residue type, secondary structure or local precision, although the number of observed NOEs in these classes varies considerably. The completeness of NOE restraints is a useful quality criterion in the course of structure refinement. The completeness per residue is more informative than the number of NOEs per residue, which makes it a useful tool to assess the quality of the NMR data set in relation to the resulting structures.
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking - 7thSpace Interactive (press release)
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking - 7thSpace Interactive (press release)
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DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking
7thSpace Interactive (press release)
Unfortunately, the experimental determination of protein-RNA complexes is tedious and difficult, both by X-ray crystallography and NMR. For many interacting proteins and RNAs the individual structures are available, enabling computational prediction of ...
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[NMR paper] Influence of the completeness of chemical shift assignments on NMR structures obtaine
Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment.
Related Articles Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment.
J Struct Funct Genomics. 2003;4(2-3):179-89
Authors: Jee J, Güntert P
Reliable automated NOE assignment and structure calculation on the basis of a largely complete, assigned input chemical shift list and a list of unassigned NOESY cross peaks has recently become feasible for routine NMR protein...
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[NMR paper] Principal components analysis of protein structure ensembles calculated using NMR dat
Principal components analysis of protein structure ensembles calculated using NMR data.
Related Articles Principal components analysis of protein structure ensembles calculated using NMR data.
J Biomol NMR. 2001 May;20(1):61-70
Authors: Howe PW
One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated...
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[NMR paper] Structure of segments of a G protein-coupled receptor: CD and NMR analysis of the Sac
Structure of segments of a G protein-coupled receptor: CD and NMR analysis of the Saccharomyces cerevisiae tridecapeptide pheromone receptor.
Related Articles Structure of segments of a G protein-coupled receptor: CD and NMR analysis of the Saccharomyces cerevisiae tridecapeptide pheromone receptor.
Biopolymers. 1998 Nov;46(6):343-57
Authors: Arshava B, Liu SF, Jiang H, Breslav M, Becker JM, Naider F
Peptides representing both loop and the sixth transmembrane regions of the alpha-factor receptor of Saccharomyces cerevisiae were synthesized by...
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[NMR paper] Defining the statistical distribution of vesicle diameters facilitates quantitative a
Defining the statistical distribution of vesicle diameters facilitates quantitative assessment of spectral narrowing from small vesicles in protein/lipid interaction studies by 2H-NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Defining the statistical distribution of vesicle diameters facilitates quantitative assessment of spectral narrowing from small vesicles in protein/lipid interaction studies by 2H-NMR.
Biochem Biophys Res Commun. 1993 May 14;192(3):1042-8
Authors: Gale...
Structure-oriented methods for protein NMR data analysis
Structure-oriented methods for protein NMR data analysis
Publication year: 2010
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 3 March 2010</br>
Guillermo A., Bermejo , Miguel, Llinás</br>
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Paramagnetic tagging for protein structure and dynamics analysis
Paramagnetic tagging for protein structure and dynamics analysis
Publication year: 2010
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 12 August 2010</br>
Peter H.J., Keizers , Marcellus, Ubbink</br>
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Completeness of NOEs in protein structure: a statistical analysis of NMR.
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