Related ArticlesNMR-Based Modeling and Refinement of Protein 3D Structures.
Methods Mol Biol. 2015;1215:351-80
Authors: Vranken WF, Vuister GW, Bonvin AM
Abstract
NMR is a well-established method to characterize the structure and dynamics of biomolecules in solution. High-quality structures can now be produced thanks to both experimental advances and computational developments that incorporate new NMR parameters and improved protocols and force fields in the structure calculation and refinement process. In this chapter, we give a short overview of the various types of NMR data that can provide structural information, and then focus on the structure calculation methodology itself. We discuss and illustrate with tutorial examples "classical" structure calculation, refinement, and structure validation approaches.
[NMR paper] Refinement of NMR structures using implicit solvent and advanced sampling techniques.
Refinement of NMR structures using implicit solvent and advanced sampling techniques.
Related Articles Refinement of NMR structures using implicit solvent and advanced sampling techniques.
J Am Chem Soc. 2004 Dec 15;126(49):16038-47
Authors: Chen J, Im W, Brooks CL
NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB)...
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[NMR paper] Sources of and solutions to problems in the refinement of protein NMR structures agai
Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force.
Related Articles Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force.
J Magn Reson. 2000 Oct;146(2):249-54
Authors: Kuszewski J, Clore GM
It is often the case that a substantial number of torsion angles (both backbone and sidechain) in structures of proteins and nucleic acids determined by NMR are found in physically unlikely and...
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[NMR paper] An approach to protein homology modelling based on an ensemble of NMR structures: app
An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.
Related Articles An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.
Protein Eng. 1995 Jul;8(7):615-25
Authors: Adzhubei AA, Laughton CA, Neidle S
A new approach has been developed to reduce multiple protein structures obtained from NMR structure analysis to a smaller number of representative structures which still reflect the structural diversity of...
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[NMR paper] Protein structure refinement based on paramagnetic NMR shifts: applications to wild-t
Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c.
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 Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c.
Protein Sci. 1995 Feb;4(2):296-305
...
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[NMR paper] Complete relaxation matrix refinement of NMR structures of proteins using analyticall
Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.
Related Articles Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.
J Biomol NMR. 1991 Sep;1(3):257-69
Authors: Mertz JE, Güntert P, Wüthrich K, Braun W
A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways....
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[NMR paper] Complete relaxation matrix refinement of NMR structures of proteins using analyticall
Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.
Related Articles Complete relaxation matrix refinement of NMR structures of proteins using analytically calculated dihedral angle derivatives of NOE intensities.
J Biomol NMR. 1991 Sep;1(3):257-69
Authors: Mertz JE, Güntert P, Wüthrich K, Braun W
A new method for refining three-dimensional (3D) NMR structures of proteins is described, which takes account of the complete relaxation pathways....
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08-21-2010 11:12 PM
[NMR paper] Refinement of the NMR structures for acyl carrier protein with scalar coupling data.
Refinement of the NMR structures for acyl carrier protein with scalar coupling data.
Related Articles Refinement of the NMR structures for acyl carrier protein with scalar coupling data.
Proteins. 1990;8(4):377-85
Authors: Kim Y, Prestegard JH
Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling...
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Detection of unrealistic molecular environments in protein structures based on expect
Abstract Understanding the relationship between protein structure and biological function is a central theme in structural biology. Advances are severely hampered by errors in experimentally determined protein structures. Detection and correction of such errors is therefore of utmost importance. Electron densities in molecular structures obey certain rules which depend on the molecular environment. Here we present and discuss a new approach that relates electron densities computed from a structural model to densities expected from prior observations on identical or closely related molecular...
NMR-Based Modeling and Refinement of Protein 3D Structures.
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