ArticleJournal of biomolecular NMR2003
The precision of NMR structure ensembles revisited.
Article in Journal of biomolecular NMR, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Core packing of well-defined X-ray and NMR structures is the same.Protein science : a publication of the Protein Society · 2022Article
- A method for validating the accuracy of NMR protein structures.Nature communications · 2020Article
- Discovery and structure of the antimicrobial lasso peptide citrocin.The Journal of biological chemistry · 2019Article
- Construction of Lasso Peptide Fusion Proteins.ACS chemical biology · 2016Article
- A community resource of experimental data for NMR / X-ray crystal structure pairs.Protein science : a publication of the Protein Society · 2016Review
- Elucidating the Specificity Determinants of the AtxE2 Lasso Peptide Isopeptidase.The Journal of biological chemistry · 2015Article
- Analysis of the structural quality of the CASD-NMR 2013 entries.Journal of biomolecular NMR · 2015Article
- CABS-flex predictions of protein flexibility compared with NMR ensembles.Bioinformatics (Oxford, England) · 2014Article
- An introduction to biological NMR spectroscopy.Molecular & cellular proteomics : MCP · 2013Review
- Recommendations of the wwPDB NMR Validation Task Force.Structure (London, England : 1993) · 2013Article
- Article
- Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology.PLoS computational biology · 2010Article
- Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo.The journal of physical chemistry. B · 2010Article
- Automated protein structure calculation from NMR data.Journal of biomolecular NMR · 2009Article
- Structural biology by NMR: structure, dynamics, and interactions.PLoS computational biology · 2008Article
- A black-box re-weighting analysis can correct flawed simulation data.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- The war of tools: how can NMR spectroscopists detect errors in their structures?Journal of biomolecular NMR · 2008Article
- Comparison of multiple crystal structures with NMR data for engrailed homeodomain.Journal of biomolecular NMR · 2008Article
- NMR and X-ray analysis of structural additivity in metal binding site-swapped hybrids of rubredoxin.BMC structural biology · 2007Article
- A global analysis of NMR distance constraints from the PDB.Journal of biomolecular NMR · 2007Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biomolecular structures provide the basis for many studies in research areas such as structure-based drug design and homology modeling. In order to use molecular coordinates it is important that they are reliable in terms of accurate description of the experimental data and in terms of the overall and local geometry. Besides these primary quality criteria an indication is needed for the uncertainty in the atomic coordinates that may arise from the dynamic behavior of the considered molecules as well as from experimental- and computational procedures. In contrast to the crystallographic B-factor, a good measure for the uncertainty in NMR-derived atomic coordinates is still not available. It has become clear in recent years that the widely used atomic Root Mean Square Deviation (RMSD), which is a measure for the precision of the data, overestimates the accuracy of NMR structure ensembles and therefore is a problematic measure for the uncertainty in the atomic coordinates. In this study we report a method that yields a more realistic estimate of the uncertainty in the atomic coordinates by maximizing the RMSD of an ensemble of structures, while maintaining the accordance with the experimentally derived data. The results indicate that the RMSD of most NMR structure ensembles can be significantly increased compromising neither geometric quality nor NMR data. This maximized RMSD therefore seems a better estimate of the true uncertainty in the atomic coordinates.
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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.