ArticleJournal of biomolecular NMR2008
The war of tools: how can NMR spectroscopists detect errors in their structures?
Article in Journal of biomolecular NMR, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed, 21 citations in OpenAlex.
- A method for validating the accuracy of NMR protein structures.Nature communications · 2020Article
- A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions.Journal of biomolecular NMR · 2016Article
- Blind testing of routine, fully automated determination of protein structures from NMR data.Structure (London, England : 1993) · 2012Article
- A quality metric for homology modeling: the H-factor.BMC bioinformatics · 2011Article
- Detection of unrealistic molecular environments in protein structures based on expected electron densities.Journal of biomolecular NMR · 2010Article
- Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.Biophysical journal · 2010Article
- The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.Journal of biomolecular NMR · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 which these tools could be applied to detect flaws in NMR structures. In particular, we investigated the variation in the scores assigned by these programs as a function of the deviation of the structures induced by errors in assignments or in the upper distance limits used. These perturbations did not distort radically the protein fold, but resulted in backbone RMS deviations up to 3 A, which is in line with errors highlighted in the available literature. We found that it is quite difficult to discriminate the structures perturbed because of misassignments from the original ones, also because the spread in score over the conformers of the original bundle is relatively large. varphi-psi distributions and normality scores related to the backbone conformation and to the distribution of side-chain dihedral angles are the most sensitive indicators of flaws.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.