Related ArticlesTorsion 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 torsion angle constraints collected by nuclear magnetic resonance (NMR) experiments performs simulated annealing by molecular dynamics in torsion angle space and uses a fast recursive algorithm to integrate the equations of motions. Torsion angle dynamics can be more efficient than molecular dynamics in Cartesian coordinate space because of the reduced number of degrees of freedom and the concomitant absence of high-frequency bond and angle vibrations, which allows for the use of longer time-steps and/or higher temperatures in the structure calculation. It also represents a significant advance over the variable target function method in torsion angle space with the REDAC strategy used by the predecessor program DIANA. DYANA computation times per accepted conformer in the "bundle" used to represent the NMR structure compare favorably with those of other presently available structure calculation algorithms, and are of the order of 160 seconds for a protein of 165 amino acid residues when using a DEC Alpha 8400 5/300 computer. Test calculations starting from conformers with random torsion angle values further showed that DYANA is capable of efficient calculation of high-quality protein structures with up to 400 amino acid residues, and of nucleic acid structures.
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...
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[NMR paper] An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.
An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.
Related Articles An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations.
J Biomol NMR. 2005 Sep;33(1):15-24
Authors: Craft JW, Legge GB
Protein structure determination using Nuclear Magnetic Resonance (NMR) requires the use of molecular dynamics programs that incorporate both NMR experimental and implicit atomic data. Atomic parameters for each amino acid type are encoded in...
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[NMR paper] Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy.
Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy.
Related Articles Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy.
J Am Chem Soc. 2005 Sep 21;127(37):12965-74
Authors: Andronesi OC, Becker S, Seidel K, Heise H, Young HS, Baldus M
It is shown that molecular structure and dynamics of a uniformly labeled membrane protein can be studied under magic-angle-spinning conditions. For this purpose, dipolar recoupling experiments...
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[NMR paper] PSEUDYANA for NMR structure calculation of paramagnetic metalloproteins using torsion
PSEUDYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics.
Related Articles PSEUDYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics.
J Biomol NMR. 1998 Nov;12(4):553-7
Authors: Banci L, Bertini I, Cremonini MA, Gori-Savellini G, Luchinat C, Wüthrich K, Güntert P
The program DYANA, for calculation of solution structures of biomolecules with an algorithm based on simulated annealing by torsion angle dynamics, has been supplemented with a...
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[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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08-22-2010 03:31 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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08-22-2010 03:03 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...