Related ArticlesAn expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments.
J Biomol NMR. 2004 Jun;29(2):111-38
Authors: Langmead CJ, Donald BR
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.
[NMR paper] A polynomial-time nuclear vector replacement algorithm for automated NMR resonance as
A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments.
Related Articles A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments.
J Comput Biol. 2004;11(2-3):277-98
Authors: Langmead CJ, Yan A, Lilien R, Wang L, Donald BR
High-throughput NMR structural biology can play an important role in structural genomics. We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of a homologous structure. These...
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[NMR paper] A systematic case study on using NMR models for molecular replacement: p53 tetrameriz
A systematic case study on using NMR models for molecular replacement: p53 tetramerization domain revisited.
Related Articles A systematic case study on using NMR models for molecular replacement: p53 tetramerization domain revisited.
Acta Crystallogr D Biol Crystallogr. 2000 Dec;56(Pt 12):1535-40
Authors: Chen YW, Clore GM
Molecular replacement using search models derived from nuclear magnetic resonance (NMR) spectroscopy has often proved problematic. It has been known for some time that the overall differences in atomic positions (r.m.s.d.)...
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11-19-2010 08:29 PM
[NMR paper] Replacement of His23 by Cys in a zinc finger of HIV-1 NCp7 led to a change in 1H NMR-
Replacement of His23 by Cys in a zinc finger of HIV-1 NCp7 led to a change in 1H NMR-derived 3D structure and to a loss of biological activity.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Replacement of His23 by Cys in a zinc finger of HIV-1 NCp7 led to a change in 1H NMR-derived 3D structure and to a loss of biological activity.
FEBS Lett. 1993 Sep 27;331(1-2):43-8
Authors: Julian N, Demene H, Morellet N, Maigret B, Roques BP
The nucleocapsid protein NCp7 of human...
Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH
Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH
Jochen Volk, Torsten Herrmann and Kurt Wüthrich
Journal of Biomolecular NMR; 2008; 41(3); pp 127 - 138
Abstract:
MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics...
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