Related ArticlesCompatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.
PLoS One. 2017;12(12):e0189700
Authors: Feng Y
Abstract
The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculating the published structures of protein-carbohydrate complexes and glycosylated proteins demonstrates that the results are comparable to the published structures which employed more complex procedures for structure calculation. Integrating the new carbohydrate parameters into the standard structure calculation protocol will facilitate three-dimensional structural study of carbohydrates and glycosylated proteins by NMR spectroscopy.
[NMR paper] Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.
Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.
Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation.
J Biomol NMR. 2015 Jul 5;
Authors: Marassi FM, Ding Y, Schwieters CD, Tian Y, Yao Y
Abstract
The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement...
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Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation
Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation
Abstract
The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot,...
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07-05-2015 02:07 AM
[NMR paper] Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations.
Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations.
Related Articles Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations.
Chem Soc Rev. 2013 Jul 25;
Authors: Toukach FV, Ananikov VP
Abstract
All living systems are comprised of four fundamental classes of macromolecules - nucleic acids, proteins, lipids, and carbohydrates (glycans). Glycans play a unique role of joining three...
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07-28-2013 07:46 PM
A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers
A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers
Abstract We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly 15N,13C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes...
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06-30-2011 05:01 AM
[NMR paper] Protein heteronuclear NMR assignments using mean-field simulated annealing.
Protein heteronuclear NMR assignments using mean-field simulated annealing.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Protein heteronuclear NMR assignments using mean-field simulated annealing.
J Magn Reson. 1997 Mar;125(1):34-42
Authors: Buchler NE, Zuiderweg ER, Wang H, Goldstein RA
A computational method for the assignment of the NMR spectra of larger (21 kDa) proteins using a set of six of the most sensitive heteronuclear multidimensional nuclear magnetic...
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08-22-2010 03:31 PM
[NMR paper] Protein heteronuclear NMR assignments using mean-field simulated annealing.
Protein heteronuclear NMR assignments using mean-field simulated annealing.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Protein heteronuclear NMR assignments using mean-field simulated annealing.
J Magn Reson. 1997 Mar;125(1):34-42
Authors: Buchler NE, Zuiderweg ER, Wang H, Goldstein RA
A computational method for the assignment of the NMR spectra of larger (21 kDa) proteins using a set of six of the most sensitive heteronuclear multidimensional nuclear magnetic...
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Journal club
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08-22-2010 03:03 PM
[NMR paper] Simulated annealing with restrained molecular dynamics using a flexible restraint pot
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints.
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 Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints.
...
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08-22-2010 02:27 PM
[NMR paper] Simulated annealing with restrained molecular dynamics using CONGEN: energy refinemen
Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha transforming growth factors.
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 Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha...
Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.
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