Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints

Paul B. Laub; Sepideh Khorasanizadeh; Heinrich Roder

doi:10.1002/pro.5560040517

Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints

Protein Science ◽

10.1002/pro.5560040517 ◽

2008 ◽

Vol 4 (5) ◽

pp. 973-982 ◽

Cited By ~ 12

Author(s):

Paul B. Laub ◽

Sepideh Khorasanizadeh ◽

Heinrich Roder

Keyword(s):

Molecular Dynamics ◽

Solution Structure ◽

Structure Refinement ◽

Distance Restraints ◽

Stochastic Boundary

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Structure refinement of oligonucleotides by molecular dynamics with nuclear overhauser effect interproton distance restraints: Application to 5′ d(C-G-T-A-C-G)2

Journal of Molecular Biology ◽

10.1016/0022-2836(86)90168-3 ◽

1986 ◽

Vol 188 (3) ◽

pp. 455-475 ◽

Cited By ~ 102

Author(s):

Lennart Nilsson ◽

G.Marius Clore ◽

Angela M. Gronenborn ◽

Axel T. Brünger ◽

Martin Karplus

Keyword(s):

Molecular Dynamics ◽

Nuclear Overhauser Effect ◽

Structure Refinement ◽

Interproton Distance ◽

Overhauser Effect ◽

Distance Restraints ◽

Nuclear Overhauser

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Faculty Opinions recommendation of Light activation of rhodopsin: insights from molecular dynamics simulations guided by solid-state NMR distance restraints.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.2426988.2061090 ◽

2010 ◽

Author(s):

James Bowie

Keyword(s):

Molecular Dynamics ◽

Solid State ◽

Molecular Dynamics Simulations ◽

Solid State Nmr ◽

Light Activation ◽

Distance Restraints ◽

Dynamics Simulations

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Effects of Urea, Tetramethyl Urea, and TrimethylamineN-Oxide on Aqueous Solution Structure and Solvation of Protein Backbones: A Molecular Dynamics Simulation Study

The Journal of Physical Chemistry B ◽

10.1021/jp9084926 ◽

2010 ◽

Vol 114 (1) ◽

pp. 557-568 ◽

Cited By ~ 128

Author(s):

Haiyan Wei ◽

Yubo Fan ◽

Yi Qin Gao

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Solution Structure ◽

Dynamics Simulation ◽

Protein Backbones

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Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from β-spectrin 1 1Edited by P. E. Wright

Journal of Molecular Biology ◽

10.1006/jmbi.1997.1044 ◽

1997 ◽

Vol 269 (3) ◽

pp. 408-422 ◽

Cited By ~ 305

Author(s):

Michael Nilges ◽

Maria J Macias ◽

Séan I O’Donoghue ◽

Hartmut Oschkinat

Keyword(s):

Solution Structure ◽

Pleckstrin Homology Domain ◽

Pleckstrin Homology ◽

Nmr Solution Structure ◽

Distance Restraints

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Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to X-ray crystallographic and NMR data

Protein Engineering Design and Selection ◽

10.1093/protein/8.11.1117 ◽

1995 ◽

Vol 8 (11) ◽

pp. 1117-1128 ◽

Cited By ~ 33

Author(s):

Aijun Li ◽

Valerie Daggett

Keyword(s):

Molecular Dynamics ◽

Solution Structure ◽

Chymotrypsin Inhibitor ◽

X Ray ◽

Chymotrypsin Inhibitor 2 ◽

Nmr Data

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Improved cryoEM-Guided Iterative Molecular Dynamics–Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction

Journal of Chemical Theory and Computation ◽

10.1021/ct500995d ◽

2015 ◽

Vol 11 (3) ◽

pp. 1337-1346 ◽

Cited By ~ 24

Author(s):

Steffen Lindert ◽

J. Andrew McCammon

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Protein Structure Prediction ◽

High Precision ◽

Structure Prediction ◽

Structure Refinement ◽

Protein Structure Refinement

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The solution structure of the intramolecular photoproduct of d(TpA) derived with the use of NMR and a combination of distance geometry and molecular dynamics

Nucleic Acids Research ◽

10.1093/nar/18.2.277 ◽

1990 ◽

Vol 18 (2) ◽

pp. 277-284 ◽

Cited By ~ 18

Author(s):

T.M.G. Koning ◽

R.J.H. Davies ◽

R. Kaptein

Keyword(s):

Molecular Dynamics ◽

Solution Structure ◽

Distance Geometry

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Crystallographic structure refinement using molecular dynamics constrained to torsion angles

Acta Crystallographica Section A Foundations of Crystallography ◽

10.1107/s0108767396095724 ◽

1996 ◽

Vol 52 (a1) ◽

pp. C84-C84

Author(s):

L. M. Rice ◽

A. T. Brünger

Keyword(s):

Molecular Dynamics ◽

Structure Refinement ◽

Crystallographic Structure ◽

Torsion Angles

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Molecular Dynamics Applied to X-ray Structure Refinement

Accounts of Chemical Research ◽

10.1021/ar010034r ◽

2002 ◽

Vol 35 (6) ◽

pp. 404-412 ◽

Cited By ~ 47

Author(s):

Axel T. Brunger ◽

Paul D. Adams

Keyword(s):

Molecular Dynamics ◽

Structure Refinement ◽

X Ray

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Lipid Bilayer Structure Refinement with Saxs/Sans Based Restrained Ensemble Molecular Dynamics

Biophysical Journal ◽

10.1016/j.bpj.2018.11.912 ◽

2019 ◽

Vol 116 (3) ◽

pp. 164a

Author(s):

Yevhen K. Cherniavskyi ◽

D. Peter Tieleman

Keyword(s):

Molecular Dynamics ◽

Lipid Bilayer ◽

Structure Refinement ◽

Bilayer Structure

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