Dynamics of the Hck-SH3 domain: Comparison of experiment with multiple molecular dynamics simulations

David A. Horita; R. Andrew Byrd; Weixing Zhang; Thomas E. Smithgall; William H. Gmeiner

doi:10.1110/ps.9.1.95

Dynamics of the Hck-SH3 domain: Comparison of experiment with multiple molecular dynamics simulations

Protein Science ◽

10.1110/ps.9.1.95 ◽

2008 ◽

Vol 9 (1) ◽

pp. 95-103 ◽

Cited By ~ 17

Author(s):

David A. Horita ◽

R. Andrew Byrd ◽

Weixing Zhang ◽

Thomas E. Smithgall ◽

William H. Gmeiner

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sh3 Domain ◽

Dynamics Simulations

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Insights into the Folding and Unfolding Processes of Wild-Type and Mutated SH3 Domain by Molecular Dynamics and Replica Exchange Molecular Dynamics Simulations

PLoS ONE ◽

10.1371/journal.pone.0064886 ◽

2013 ◽

Vol 8 (5) ◽

pp. e64886 ◽

Cited By ~ 6

Author(s):

Wen-Ting Chu ◽

Ji-Long Zhang ◽

Qing-Chuan Zheng ◽

Lin Chen ◽

Hong-Xing Zhang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sh3 Domain ◽

Replica Exchange ◽

Wild Type ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Simulations

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Docking and molecular dynamics simulations of the Fyn-SH3 domain with free and phospholipid bilayer-associated 18.5-kDa myelin basic protein (MBP)-Insights into a noncanonical and fuzzy interaction

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25295 ◽

2017 ◽

Vol 85 (7) ◽

pp. 1336-1350 ◽

Cited By ~ 1

Author(s):

Kyrylo Bessonov ◽

Kenrick A. Vassall ◽

George Harauz

Keyword(s):

Molecular Dynamics ◽

Myelin Basic Protein ◽

Molecular Dynamics Simulations ◽

Basic Protein ◽

Sh3 Domain ◽

Phospholipid Bilayer ◽

Dynamics Simulations

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Molecular dynamics simulations of a highly charged peptide from an SH3 domain: Possible sequence-function relationship

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.1118 ◽

2001 ◽

Vol 45 (1) ◽

pp. 4-15 ◽

Cited By ~ 9

Author(s):

Brent P. Krueger ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sh3 Domain ◽

Function Relationship ◽

Dynamics Simulations

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488.1-Pos Board # B29.1 – Formation of the Folding Nucleus of src-SH3 Domain from Denatured Conformations Investigated Through Biased Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/s0006-3495(03)70113-1 ◽

2003 ◽

Vol 84 (5) ◽

pp. 3488

Author(s):

Giovanni Settanni ◽

Joerg Gsponer ◽

Amedeo Caflisch

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sh3 Domain ◽

Folding Nucleus ◽

Dynamics Simulations

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Formation of the Folding Nucleus of an SH3 Domain Investigated by Loosely Coupled Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/s0006-3495(04)74238-1 ◽

2004 ◽

Vol 86 (3) ◽

pp. 1691-1701 ◽

Cited By ~ 20

Author(s):

G. Settanni ◽

J. Gsponer ◽

A. Caflisch

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sh3 Domain ◽

Loosely Coupled ◽

Folding Nucleus ◽

Dynamics Simulations

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The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations

BMC Structural Biology ◽

10.1186/1472-6807-11-46 ◽

2011 ◽

Vol 11 (1) ◽

pp. 46

Author(s):

Nathalie Duclert-Savatier ◽

Leandro Martínez ◽

Michael Nilges ◽

Thérèse E Malliavin

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Sh3 Domain ◽

Dynamics Simulations ◽

Nmr Restraints

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Molecular dynamics simulations from putative transition states of α-spectrin SH3 domain

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21491 ◽

2007 ◽

Vol 69 (3) ◽

pp. 536-550 ◽

Cited By ~ 13

Author(s):

Xavier Periole ◽

Michele Vendruscolo ◽

Alan E. Mark

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Transition States ◽

Sh3 Domain ◽

Dynamics Simulations

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Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

Molecular Physics ◽

10.1080/002689700162045 ◽

2000 ◽

Vol 98 (11) ◽

pp. 701-707

Author(s):

Alessandro Sergi, Mauro Ferrario, Francesco Bu

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Ab Initio Molecular Dynamics ◽

Dynamics Simulations

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Tracer diffusion in perfectly aligned liquid crystalline phases Kinetic theory and molecular dynamics simulations

Molecular Physics ◽

10.1080/00268979709482789 ◽

1997 ◽

Vol 91 (6) ◽

pp. 993-1003 ◽

Cited By ~ 1

Author(s):

ANJALI KHARE ◽

DAVID KOFKE ◽

GLENN EVANS

Keyword(s):

Molecular Dynamics ◽

Kinetic Theory ◽

Molecular Dynamics Simulations ◽

Liquid Crystalline ◽

Tracer Diffusion ◽

Crystalline Phases ◽

Liquid Crystalline Phases ◽

Dynamics Simulations

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ERRATUM Molecular dynamics simulations of liquid crystal phases using atomistic potentials

Molecular Physics ◽

10.1080/002689798167430 ◽

1998 ◽

Vol 95 (1) ◽

pp. 121-121

Author(s):

CARL MCBRIDE MARK R. WILSON JUDITH A. K.

Keyword(s):

Molecular Dynamics ◽

Liquid Crystal ◽

Molecular Dynamics Simulations ◽

Crystal Phases ◽

Dynamics Simulations ◽

Liquid Crystal Phases

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