ArticleJournal of magnetic resonance (San Diego, Calif. : 1997)2009
Improvement and analysis of computational methods for prediction of residual dipolar couplings.
Article in Journal of magnetic resonance (San Diego, Calif. : 1997), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Reweighting methods for elucidation of conformation ensembles of proteins.Current opinion in structural biology · 2022Review
- Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints.Biophysical reviews · 2022Review
- Assessing Structural Preferences of Unstructured Protein Regions by NMR.Biophysical journal · 2019Article
- Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques.Biomolecules · 2019Review
- Linkage via K27 Bestows Ubiquitin Chains with Unique Properties among Polyubiquitins.Structure (London, England : 1993) · 2016Article
- Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.Physical chemistry chemical physics : PCCP · 2016Article
- Linkage-specific conformational ensembles of non-canonical polyubiquitin chains.Physical chemistry chemical physics : PCCP · 2016Article
- Information content of long-range NMR data for the characterization of conformational heterogeneity.Journal of biomolecular NMR · 2015Article
- FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data.Journal of biomolecular NMR · 2015Article
- Capping motifs stabilize the leucine-rich repeat protein PP32 and rigidify adjacent repeats.Protein science : a publication of the Protein Society · 2014Article
- New opportunities for tensor-free calculations of residual dipolar couplings for the study of protein dynamics.Journal of biomolecular NMR · 2014Review
- Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.Journal of biomolecular NMR · 2013Article
- Recovering a representative conformational ensemble from underdetermined macromolecular structural data.Journal of the American Chemical Society · 2013Article
- Examination of matrix metalloproteinase-1 in solution: a preference for the pre-collagenolysis state.The Journal of biological chemistry · 2013Article
- Comparative studies of disordered proteins with similar sequences: application to Aβ40 and Aβ42.Biophysical journal · 2013Article
- Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings.Journal of biomolecular NMR · 2012Article
- Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects.Progress in nuclear magnetic resonance spectroscopy · 2011Review
- Searching and optimizing structure ensembles for complex flexible sugars.Journal of the American Chemical Society · 2011Article
- Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media?Journal of biomolecular NMR · 2011Article
- Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes.Proteins · 2011Article
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3 authors.
Funding
Abstract
We describe a new, computationally efficient method for computing the molecular alignment tensor based on the molecular shape. The increase in speed is achieved by re-expressing the problem as one of numerical integration, rather than a simple uniform sampling (as in the PALES method), and by using a convex hull rather than a detailed representation of the surface of a molecule. This method is applicable to bicelles, PEG/hexanol, and other alignment media that can be modeled by steric restrictions introduced by a planar barrier. This method is used to further explore and compare various representations of protein shape by an equivalent ellipsoid. We also examine the accuracy of the alignment tensor and residual dipolar couplings (RDC) prediction using various ab initio methods. We separately quantify the inaccuracy in RDC prediction caused by the inaccuracy in the orientation and in the magnitude of the alignment tensor, concluding that orientation accuracy is much more important in accurate prediction of RDCs.
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