Literature DB >> 25652903

Fitting alignment tensor components to experimental RDCs, CSAs and RQCs.

Lukas N Wirz1, Jane R Allison.   

Abstract

Residual dipolar couplings, chemical shift anisotropies and quadrupolar couplings provide information about the orientation of inter-spin vectors and the anisotropic contribution of the local environment to the chemical shifts of nuclei, respectively. Structural interpretation of these observables requires parameterization of their angular dependence in terms of an alignment tensor. We compare and evaluate two algorithms for generating the optimal alignment tensor for a given molecular structure and set of experimental data, namely SVD (Losonczi et al. in J Magn Reson 138(2):334-342, 1999), which scales as [Formula: see text], and the linear least squares algorithm (Press et al. in Numerical recipes in C. The art of scientific computing, 2nd edn. Cambridge University Press, Cambridge, 1997), which scales as [Formula: see text].

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Year:  2015        PMID: 25652903     DOI: 10.1007/s10858-015-9907-x

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  9 in total

1.  Orientation restraints in molecular dynamics simulations using time and ensemble averaging.

Authors:  B Hess; R M Scheek
Journal:  J Magn Reson       Date:  2003-09       Impact factor: 2.229

Review 2.  Residual dipolar couplings in NMR structure analysis.

Authors:  Rebecca S Lipsitz; Nico Tjandra
Journal:  Annu Rev Biophys Biomol Struct       Date:  2004

Review 3.  Residual dipolar couplings in structure determination of biomolecules.

Authors:  J H Prestegard; C M Bougault; A I Kishore
Journal:  Chem Rev       Date:  2004-08       Impact factor: 60.622

4.  New functionalities in the GROMOS biomolecular simulation software.

Authors:  Anna-Pitschna E Kunz; Jane R Allison; Daan P Geerke; Bruno A C Horta; Philippe H Hünenberger; Sereina Riniker; Nathan Schmid; Wilfred F van Gunsteren
Journal:  J Comput Chem       Date:  2011-11-11       Impact factor: 3.376

5.  Structural constraints from residual tensorial couplings in high resolution NMR without an explicit term for the alignment tensor.

Authors:  S Moltke; S Grzesiek
Journal:  J Biomol NMR       Date:  1999-09       Impact factor: 2.835

6.  GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories.

Authors:  Andreas P Eichenberger; Jane R Allison; Jožica Dolenc; Daan P Geerke; Bruno A C Horta; Katharina Meier; Chris Oostenbrink; Nathan Schmid; Denise Steiner; Dongqi Wang; Wilfred F van Gunsteren
Journal:  J Chem Theory Comput       Date:  2011-09-16       Impact factor: 6.006

7.  Biomolecular structure refinement using the GROMOS simulation software.

Authors:  Nathan Schmid; Jane R Allison; Jožica Dolenc; Andreas P Eichenberger; Anna-Pitschna E Kunz; Wilfred F van Gunsteren
Journal:  J Biomol NMR       Date:  2011-08-20       Impact factor: 2.835

8.  Conventions for the reporting of nuclear magnetic shielding (or shift) tensors suggested by participants in the NATO ARW on NMR shielding constants at the University of Maryland, College Park, July 1992.

Authors:  J Mason
Journal:  Solid State Nucl Magn Reson       Date:  1993-10       Impact factor: 2.293

9.  Order matrix analysis of residual dipolar couplings using singular value decomposition.

Authors:  J A Losonczi; M Andrec; M W Fischer; J H Prestegard
Journal:  J Magn Reson       Date:  1999-06       Impact factor: 2.229

  9 in total
  1 in total

1.  Configuration determination by residual dipolar couplings: accessing the full conformational space by molecular dynamics with tensorial constraints.

Authors:  Pavleta Tzvetkova; Ulrich Sternberg; Thomas Gloge; Armando Navarro-Vázquez; Burkhard Luy
Journal:  Chem Sci       Date:  2019-07-29       Impact factor: 9.825

  1 in total

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