ArticleJournal of biomolecular NMR2005
Estimating the accuracy of protein structures using residual dipolar couplings.
Article in Journal of biomolecular NMR, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 16 citations in OpenAlex.
- A method for validating the accuracy of NMR protein structures.Nature communications · 2020Article
- Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR.RNA (New York, N.Y.) · 2020Article
- Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2.Scientific reports · 2019Article
- Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists.Computational and structural biotechnology journal · 2017Review
- Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics.Protein science : a publication of the Protein Society · 2014Article
- Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?Journal of biomolecular NMR · 2011Article
- Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.Accounts of chemical research · 2009Article
- Structure discrimination for the C-terminal domain of Escherichia coli trigger factor in solution.Journal of biomolecular NMR · 2008Article
- Predicting 13Calpha chemical shifts for validation of protein structures.Journal of biomolecular NMR · 2007Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H-15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable R values virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable R values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E.
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