The present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor-NIH biomolecular structure determination package. In combination with an improved treatment of selected non-bonded interactions between atoms three bonds apart, such as those involving methyl hydrogens, and a previously developed term that affects the system's gyration volume, the new parameters are tested using structure calculations on 30 proteins with restraints derived from nuclear magnetic resonance data. Using modern structure validation criteria, including several formally adopted by the Protein Data Bank, and a clear measure of structural accuracy, the results show superior performance relative to previous Xplor-NIH implementations. Additionally, the Xplor-NIH structures compare favorably against originally determined NMR models.
[NMR paper] Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.
Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing.
Related Articles Compatible 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,...
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12-13-2017 06:15 PM
[NMR paper] Protein Structure Elucidation from NMR Data with the Program Xplor-NIH.
Protein Structure Elucidation from NMR Data with the Program Xplor-NIH.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Protein Structure Elucidation from NMR Data with the Program Xplor-NIH.
Methods Mol Biol. 2018;1688:311-340
Authors: Bermejo GA, Schwieters CD
Abstract
Xplor-NIH is a popular software package for biomolecular structure determination from NMR (and other) experimental data. This chapter illustrates its use with...
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11-21-2017 10:10 PM
Xplor-NIH for molecular structure determination from NMR and other data sources
Xplor-NIH for molecular structure determination from NMR and other data sources
Abstract
Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options for using residual dipolar coupling data in structure calculations. Further, we discuss new developments in the implementation of strict symmetry for the calculation of symmetric homo-oligomers, and in the representation of the system as an...
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09-18-2017 10:41 AM
[NMR paper] Xplor-NIH for Molecular Structure Determination from NMR and Other Data Sources.
Xplor-NIH for Molecular Structure Determination from NMR and Other Data Sources.
Related Articles Xplor-NIH for Molecular Structure Determination from NMR and Other Data Sources.
Protein Sci. 2017 Aug 02;:
Authors: Schwieters CD, Bermejo GA, Clore GM
Abstract
Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options for using...
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08-03-2017 11:48 AM
Xplor-NIH for Molecular Structure Determination from NMR and Other Data Sources
Xplor-NIH for Molecular Structure Determination from NMR and Other Data Sources
Abstract
Xplor-NIH is a popular software package for biomolecular structure determination from nuclear magnetic resonance (NMR) and other data sources. Here, some of Xplor-NIH's most useful data-associated energy terms are reviewed, including newer alternative options for using residual dipolar coupling data in structure calculations. Further, we discuss new developments in the implementation of strict symmetry for the calculation of symmetric homo-oligomers, and in the representation of the system as an...
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08-02-2017 02:19 PM
[NMR paper] Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder.
Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder.
Related Articles Comparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder.
J Biomol Struct Dyn. 2017 Jul 17;:1-34
Authors: Faraggi E, Dunker K, Sussman J, Kloczkowski A
Abstract
Disordered protein chains and segments are fast becoming a major pathway for our understanding of biological function, especially in more evolved species. However, the standard definition of disordered residues: the inability to constrain...
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07-19-2017 12:46 AM
[NMR paper] Determination of protein structures consistent with NMR order parameters.
Determination of protein structures consistent with NMR order parameters.
Related Articles Determination of protein structures consistent with NMR order parameters.
J Am Chem Soc. 2004 Jul 7;126(26):8090-1
Authors: Best RB, Vendruscolo M
Order parameters obtained from NMR experiments characterize distributions of bond vector orientations. Their interpretation, however, usually requires the assumption of a particular motional model. We propose a multiple-copy simulation method in which the experimental order parameters are used as restraints in...
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11-24-2010 09:51 PM
[Question from NMRWiki Q&A forum] How to keep XPLOR structure calculation from exploding?
How to keep XPLOR structure calculation from exploding?
Trying to calculate a structure using sa.inp script and the energy in the cooling loop increases instead of going down.
In the end there is a message
****&&&& rerun job with smaller timestep (i.e., 0.003)But making the timestep smaller does not help. Could anyone suggest where to look?
edit: I've also commented out my restrains thinking that maybe my noe's are too whacky, but still structure diverges.
Xplor-NIH: Better parameters and protocols for NMR protein structure determination
Linear Mode
