Related ArticlesTorsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.
J Magn Reson. 1997 Jan;124(1):154-64
Authors: Stein EG, Rice LM, Brünger AT
Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances and J-coupling-constant-derived dihedral angle restraints. Compared to two other commonly used algorithms, molecular dynamics in Cartesian space and metric-matrix geometry combined with Cartesian molecular dynamics, the method shows increased computational efficiency and success rate for large proteins, and it shows a dramatically increased radius of convergence for DNA. The torsion-angle molecular dynamics algorithm starts from an extended strand conformation and proceeds in four stages: high-temperature torsion-angle molecular dynamics, slow-cooling torsion-angle molecular dynamics, Cartesian molecular dynamics, and minimization. Tests were carried out using experimental NMR data for protein G, interleukin-8, villin 14T, and a 12 base-pair duplex of DNA, and simulated NMR data for bovine pancreatic trypsin inhibitor. For villin 14T , a monomer consisting of 126 residues, structure determination by torsion-angle molecular dynamics has a success rate of 85%, a more than twofold improvement over other methods. In the case of the 12 base-pair DNA duplex, torsion-angle molecular dynamics had a success rate of 52% while Cartesian molecular dynamics and metric-matrix distance geometry always failed.
Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space
Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space
Abstract A method is introduced to represent an ensemble of conformers of a protein by a single structure in torsion angle space that lies closest to the averaged Cartesian coordinates while maintaining perfect covalent geometry and on average equal steric quality and an equally good fit to the experimental (e.g. NMR) data as the individual conformers of the ensemble. The single representative â??regmean structureâ?? is obtained by simulated annealing in torsion angle space with the...
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Site-Specific ?- and ?-Torsion Angle Determination in a Uniformly/Extensively 13C- and 15N-Labeled Peptide
Site-Specific ?- and ?-Torsion Angle Determination in a Uniformly/Extensively 13C- and 15N-Labeled Peptide
Publication year: 2011
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 17 August 2011</br>
Sungsool, Wi , Justin, Spano</br>
A solid-state rotational-echo double resonance (REDOR) NMR method was introduced to identify the ?- and ?-torsion angle from a 1H–15N or 1H–13C? spin system of alanine-like residues in a selectively, uniformly, or extensively 15N-/13C-labeled peptide. When a C?(i) or a 15N peak is site-specifically obtainable in the...
Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins
Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins
Raquel Godoy-Ruiz, Chenyun Guo and Vitali Tugarinov
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja1083656/aop/images/medium/ja-2010-083656_0009.gif
Journal of the American Chemical Society
DOI: 10.1021/ja1083656
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/hxZ4cabF688
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[NMR paper] Torsion angle dynamics for NMR structure calculation with the new program DYANA.
Torsion angle dynamics for NMR structure calculation with the new program DYANA.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Torsion angle dynamics for NMR structure calculation with the new program DYANA.
J Mol Biol. 1997 Oct 17;273(1):283-98
Authors: Güntert P, Mumenthaler C, Wüthrich K
The new program DYANA (DYnamics Algorithm for Nmr Applications) for efficient calculation of three-dimensional protein and nucleic acid structures from distance constraints and...
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08-22-2010 05:08 PM
[NMR paper] Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculatio
Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation.
J Magn Reson. 1997 Jan;124(1):154-64
Authors: Stein EG, Rice LM, Brünger AT
Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances and...
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0
08-22-2010 03:31 PM
[NMR paper] Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by
Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement.
Protein Sci. 1996...