ArticleJournal of biomolecular NMR2004
An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments.
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, 65 citations in OpenAlex.
- RASP: rapid and robust backbone chemical shift assignments from protein structure.Journal of biomolecular NMR · 2014Article
- Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.Molecules (Basel, Switzerland) · 2013Article
- HASH: a program to accurately predict protein Hα shifts from neighboring backbone shifts.Journal of biomolecular NMR · 2013Article
- 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
- Backbone resonance assignment and order tensor estimation using residual dipolar couplings.Journal of biomolecular NMR · 2011Article
- NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.The computer journal · 2011Article
- RDC derived protein backbone resonance assignment using fragment assembly.Journal of biomolecular NMR · 2011Article
- Structure-oriented methods for protein NMR data analysis.Progress in nuclear magnetic resonance spectroscopy · 2010Review
- Robust structure-based resonance assignment for functional protein studies by NMR.Journal of biomolecular NMR · 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
- NOEnet--use of NOE networks for NMR resonance assignment of proteins with known 3D structure.Bioinformatics (Oxford, England) · 2009Article
- Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data.Journal of biomolecular NMR · 2008Article
- Graphical interpretation of Boolean operators for protein NMR assignments.Journal of biomolecular NMR · 2008Article
- Contact replacement for NMR resonance assignment.Bioinformatics (Oxford, England) · 2008Article
- Structure-based protein NMR assignments using native structural ensembles.Journal of biomolecular NMR · 2008Article
- Deuterated protein folds obtained directly from unassigned nuclear overhauser effect data.Journal of the American Chemical Society · 2008Article
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2 authors at 1 institution in 1 country.
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Abstract
We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of an homologous structure. Our algorithm performs Nuclear Vector Replacement (NVR) by Expectation/Maximization (EM) to compute assignments. NVR correlates experimentally-measured NH residual dipolar couplings (RDCs) and chemical shifts to a given a priori whole-protein 3D structural model. The algorithm requires only uniform (15)N-labelling of the protein, and processes unassigned H(N)-(15)N HSQC spectra, H(N)-(15)N RDCs, and sparse H(N)-H(N) NOE's (d(NN)s). NVR runs in minutes and efficiently assigns the (H(N),(15)N) backbone resonances as well as the sparse d(NN)s from the 3D (15)N-NOESY spectrum, in O (n(3)) time. The algorithm is demonstrated on NMR data from a 76-residue protein, human ubiquitin, matched to four structures, including one mutant (homolog), determined either by X-ray crystallography or by different NMR experiments (without RDCs). NVR achieves an average assignment accuracy of over 99%. We further demonstrate the feasibility of our algorithm for different and larger proteins, using different combinations of real and simulated NMR data for hen lysozyme (129 residues) and streptococcal protein G (56 residues), matched to a variety of 3D structural models.
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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.