ArticleJournal of biomolecular NMR2004
Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure.
Article in Journal of biomolecular NMR, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution.PLoS computational biology · 2021Article
- Integrating NOE and RDC using sum-of-squares relaxation for protein structure determination.Journal of biomolecular NMR · 2017Article
- Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings.Journal of biomolecular NMR · 2014Article
- HASH: a program to accurately predict protein Hα shifts from neighboring backbone shifts.Journal of biomolecular NMR · 2013Article
- Article
- A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data.Journal of computational biology : a journal of computational molecular cell biology · 2011Article
- Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data.Journal of biomolecular NMR · 2011Article
- A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers.Protein science : a publication of the Protein Society · 2011Article
- Simultaneous structure and dynamics of a membrane protein using REDCRAFT: membrane-bound form of Pf1 coat protein.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2010Article
- High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.Journal of biomolecular NMR · 2009Article
- Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints.Progress in nuclear magnetic resonance spectroscopy · 2009Article
- 16-fold degeneracy of peptide plane orientations from residual dipolar couplings: analytical treatment and implications for protein structure determination.Journal of the American Chemical Society · 2008Article
- De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media.Journal of biomolecular NMR · 2008Article
- REDCRAFT: a tool for simultaneous characterization of protein backbone structure and motion from RDC data.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2008Article
- Continuity conditions and torsion angles from ssNMR orientational restraints.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2008Article
- A HAUSDORFF-BASED NOE ASSIGNMENT ALGORITHM USING PROTEIN BACKBONE DETERMINED FROM RESIDUAL DIPOLAR COUPLINGS AND ROTAMER PATTERNS.Computational systems bioinformatics. Computational Systems Bioinformatics Conference · 2008Article
- HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections.Journal of biomolecular NMR · 2007Article
- 1H, 15N and 13C Backbone resonance assignments of the 37 kDa surface antigen protein Bd37 from Babesia divergens.Journal of biomolecular NMR · 2005Article
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2 authors.
Funding
Abstract
We have derived a quartic equation for computing the direction of an internuclear vector from residual dipolar couplings (RDCs) measured in two aligning media, and two simple trigonometric equations for computing the backbone (phi,psi) angles from two backbone vectors in consecutive peptide planes. These equations make it possible to compute, exactly and in constant time, the backbone (phi,psi) angles for a residue from RDCs in two media on any single backbone vector type. Building upon these exact solutions we have designed a novel algorithm for determining a protein backbone substructure consisting of alpha-helices and beta-sheets. Our algorithm employs a systematic search technique to refine the conformation of both alpha-helices and beta-sheets and to determine their orientations using exclusively the angular restraints from RDCs. The algorithm computes the backbone substructure employing very sparse distance restraints between pairs of alpha-helices and beta-sheets refined by the systematic search. The algorithm has been demonstrated on the protein human ubiquitin using only backbone NH RDCs, plus twelve hydrogen bonds and four NOE distance restraints. Further, our results show that both the global orientations and the conformations of alpha-helices and beta-strands can be determined with high accuracy using only two RDCs per residue. The algorithm requires, as its input, backbone resonance assignments, the identification of alpha-helices and beta-sheets as well as sparse NOE distance and hydrogen bond restraints.
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