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Literature DB >> 22910850

Parametrisation of time-averaged distance restraints in MD simulations.

A P Nanzer¹, W F van Gunsteren, A E Torda.

Abstract

Time-averaged restraints in molecular dynamics simulations offer a means to account for the averaging that is implicit in NMR spectroscopic data. We present a systematic investigation of the parameters which characterise time-averaged distance restraints. Using previously published data for a small protein, chymotrypsin inhibitor 2, we identify conditions which can lead to undesirable heating or which grossly distort the dynamics of the system.

Year: 1995 PMID： 22910850 DOI： 10.1007/BF00197812

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

13 in total

1. Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat.

Authors: A E Torda; R M Scheek; W F van Gunsteren
Journal: J Mol Biol Date: 1990-07-05 Impact factor: 5.469

2. A reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints.

Authors: A P Nanzer; F M Poulsen; W F van Gunsteren; A E Torda
Journal: Biochemistry Date: 1994-12-06 Impact factor: 3.162

3. How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches.

Authors: D A Pearlman
Journal: J Biomol NMR Date: 1994-01 Impact factor: 2.835

4. The determination of the three-dimensional structure of barley serine proteinase inhibitor 2 by nuclear magnetic resonance, distance geometry and restrained molecular dynamics.

Authors: G M Clore; A M Gronenborn; M Kjaer; F M Poulsen
Journal: Protein Eng Date: 1987 Aug-Sep

5. Structure refinement using time-averaged J-coupling constant restraints.

Authors: A E Torda; R M Brunne; T Huber; H Kessler; W F van Gunsteren
Journal: J Biomol NMR Date: 1993-01 Impact factor: 2.835

6. Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data.

Authors: U Schmitz; N B Ulyanov; A Kumar; T L James
Journal: J Mol Biol Date: 1993-11-20 Impact factor: 5.469

7. A protein structure from nuclear magnetic resonance data. lac repressor headpiece.

Authors: R Kaptein; E R Zuiderweg; R M Scheek; R Boelens; W F van Gunsteren
Journal: J Mol Biol Date: 1985-03-05 Impact factor: 5.469

8. Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance.

Authors: K Wüthrich; M Billeter; W Braun
Journal: J Mol Biol Date: 1983-10-05 Impact factor: 5.469

9. Accurate measurements of coupling constants from two-dimensional nuclear magnetic resonance spectra of proteins and determination of phi-angles.

Authors: S Ludvigsen; K V Andersen; F M Poulsen
Journal: J Mol Biol Date: 1991-02-20 Impact factor: 5.469

10. Refinement of the three-dimensional solution structure of barley serine proteinase inhibitor 2 and comparison with the structures in crystals.

Authors: S Ludvigsen; H Y Shen; M Kjaer; J C Madsen; F M Poulsen
Journal: J Mol Biol Date: 1991-12-05 Impact factor: 5.469

12 in total

1. An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation.

Authors: Denise Steiner; Wilfred F van Gunsteren
Journal: Eur Biophys J Date: 2012-06-16 Impact factor: 1.733

2. Molecular dynamics simulation using weak-coupling NOE distance restraining.

Authors: A P Nanzer; T Huber; A E Torda; W F van Gunsteren
Journal: J Biomol NMR Date: 1996-10 Impact factor: 2.835

3. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

Authors: Jozica Dolenc; John H Missimer; Michel O Steinmetz; Wilfred F van Gunsteren
Journal: J Biomol NMR Date: 2010-06-04 Impact factor: 2.835

4. FINGAR: A new genetic algorithm-based method for fitting NMR data.

Authors: D A Pearlman
Journal: J Biomol NMR Date: 1996-07 Impact factor: 2.835

5. On using oscillating time-dependent restraints in MD simulation.

Authors: Bettina Keller; Markus Christen; Chris Oostenbrink; Wilfred F van Gunsteren
Journal: J Biomol NMR Date: 2006-12-16 Impact factor: 2.835

6. Biomolecular structure refinement based on adaptive restraints using local-elevation simulation.

Authors: Markus Christen; Bettina Keller; Wilfred F van Gunsteren
Journal: J Biomol NMR Date: 2007-10-11 Impact factor: 2.835

7. The dynamic NMR structure of the T psi C-loop: implications for the specificity of tRNA methylation.

Authors: L J Yao; T L James; J T Kealey; D V Santi; U Schmitz
Journal: J Biomol NMR Date: 1997-04 Impact factor: 2.835

8. Time-averaged order parameter restraints in molecular dynamics simulations.

Authors: Niels Hansen; Fabian Heller; Nathan Schmid; Wilfred F van Gunsteren
Journal: J Biomol NMR Date: 2014-10-14 Impact factor: 2.835

9. On the use of time-averaging restraints when deriving biomolecular structure from ³J -coupling values obtained from NMR experiments.

Authors: Lorna J Smith; Wilfred F van Gunsteren; Niels Hansen
Journal: J Biomol NMR Date: 2016-09-15 Impact factor: 2.835

10. Structure and dynamics of the Abeta(21-30) peptide from the interplay of NMR experiments and molecular simulations.

Authors: Nicolas L Fawzi; Aaron H Phillips; Jory Z Ruscio; Michaeleen Doucleff; David E Wemmer; Teresa Head-Gordon
Journal: J Am Chem Soc Date: 2008-04-16 Impact factor: 15.419