Transition State Ensemble for the Folding of B Domain of Protein A:  A Comparison of Distributed Molecular Dynamics Simulations with Experiments

Protein A ◽

State Ensemble ◽

Dynamics Simulations ◽

Transition State Ensemble

Reconstruction of the src-SH3 Protein Domain Transition State Ensemble using Multiscale Molecular Dynamics Simulations

Journal of Molecular Biology ◽

10.1016/j.jmb.2005.05.017 ◽

2005 ◽

Vol 350 (5) ◽

pp. 1035-1050 ◽

Cited By ~ 62

Author(s):

Feng Ding ◽

Weihua Guo ◽

Nikolay V. Dokholyan ◽

Eugene I. Shakhnovich ◽

Joan-Emma Shea

Keyword(s):

Molecular Dynamics ◽

Transition State ◽

Protein Domain ◽

State Ensemble ◽

Dynamics Simulations ◽

Transition State Ensemble

Molecular Dynamics Simulations Applied to Structural and Dynamical Transitions of the Huntingtin Protein: A Review

ACS Chemical Neuroscience ◽

10.1021/acschemneuro.9b00561 ◽

2019 ◽

Vol 11 (2) ◽

pp. 105-120 ◽

Cited By ~ 1

Author(s):

Sanda Nastasia Moldovean ◽

Vasile Chiş

Keyword(s):

Molecular Dynamics ◽

Protein A ◽

Huntingtin Protein ◽

Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Cytidine Deaminase: From Stabilization of Transition State Analogues to Catalytic Mechanisms

The Journal of Physical Chemistry B ◽

10.1021/jp037529d ◽

2004 ◽

Vol 108 (7) ◽

pp. 2477-2483 ◽

Cited By ~ 7

Author(s):

Qin Xu ◽

Hong Guo

Keyword(s):

Molecular Dynamics ◽

Transition State ◽

Cytidine Deaminase ◽

Quantum Mechanical ◽

Transition State Analogues ◽

Catalytic Mechanisms ◽

Comparison of transition state theory rate constants for internal conformational motion with those obtained from molecular dynamics simulations

Polymer ◽

10.1016/s1089-3156(00)00027-1 ◽

2002 ◽

Vol 43 (2) ◽

pp. 615-620

Author(s):

B.C. Hathorn ◽

B.G. Sumpter ◽

D.W. Noid

Keyword(s):

Molecular Dynamics ◽

Transition State ◽

Rate Constants ◽

Transition State Theory ◽

State Theory ◽

Conformational Motion ◽

Unfolding transition state and intermediates of the tumor suppressor p16 INK4a investigated by molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20953 ◽

2006 ◽

Vol 64 (1) ◽

pp. 178-192 ◽

Cited By ~ 13

Author(s):

Gianluca Interlandi ◽

Giovanni Settanni ◽

Amedeo Caflisch

Keyword(s):

Molecular Dynamics ◽

Tumor Suppressor ◽

Transition State ◽

P16 Ink4a ◽

Faculty Opinions recommendation of Molecular dynamics simulations of protein folding from the transition state.

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

10.3410/f.1007230.89857 ◽

2002 ◽

Author(s):

Themis Lazaridis

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Transition State ◽

Determination of thermal intermediate state ensemble of box 5 with restrained molecular dynamics simulations

Computational and Theoretical Chemistry ◽

10.1016/j.comptc.2011.10.004 ◽

2011 ◽

Vol 978 (1-3) ◽

pp. 152-159 ◽

Cited By ~ 1

Author(s):

Liling Zhao ◽

Zhijun Liu ◽

Zanxia Cao ◽

Haiyan Liu ◽

Jihua Wang

Keyword(s):

Molecular Dynamics ◽

Intermediate State ◽

State Ensemble ◽

Dynamics Simulations ◽

Restrained Molecular Dynamics

Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations

PLoS Computational Biology ◽

10.1371/journal.pcbi.1002137 ◽

2011 ◽

Vol 7 (9) ◽

pp. e1002137 ◽

Cited By ~ 6

Author(s):

Lipi Thukral ◽

Isabella Daidone ◽

Jeremy C. Smith

Keyword(s):

Molecular Dynamics ◽

Transition State ◽

Peptide Folding ◽

Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with ϕ value restraints

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.10595 ◽

2003 ◽

Vol 54 (3) ◽

pp. 513-525 ◽

Cited By ~ 37

Author(s):

Emanuele Paci ◽

Claire T. Friel ◽

Kresten Lindorff-Larsen ◽

Sheena E. Radford ◽

Martin Karplus ◽

...

Keyword(s):

Molecular Dynamics ◽

Transition State ◽

Molecular dynamics simulations of protein folding from the transition state

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.092686399 ◽

2002 ◽

Vol 99 (10) ◽

pp. 6719-6724 ◽

Cited By ~ 95

Author(s):

J. Gsponer ◽

A. Caflisch

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Transition State ◽