Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

Jian Zhang; Yu Liang; Yang Zhang

doi:10.1016/j.str.2011.09.022

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling

Structure ◽

10.1016/j.str.2011.09.022 ◽

2011 ◽

Vol 19 (12) ◽

pp. 1784-1795 ◽

Cited By ~ 201

Author(s):

Jian Zhang ◽

Yu Liang ◽

Yang Zhang

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Refinement ◽

Atomic Level ◽

Protein Structure Refinement

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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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Protein structure refinement via molecular-dynamics simulations: What works and what does not?

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24871 ◽

2015 ◽

Vol 84 ◽

pp. 282-292 ◽

Cited By ~ 37

Author(s):

Michael Feig ◽

Vahid Mirjalili

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Structure Refinement ◽

Protein Structure Refinement ◽

What Works ◽

Dynamics Simulations

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Faculty Opinions recommendation of Experimental accuracy in protein structure refinement via molecular dynamics simulations.

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

10.3410/f.734614719.793556856 ◽

2019 ◽

Author(s):

Ken Dill ◽

Alberto Pérez

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Structure Refinement ◽

Experimental Accuracy ◽

Protein Structure Refinement ◽

Dynamics Simulations

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Cryoem-Guided Iterative Molecular Dynamics - Rosetta Protein Structure Refinement Protocol Improves Protein Model Quality

Biophysical Journal ◽

10.1016/j.bpj.2015.11.1857 ◽

2016 ◽

Vol 110 (3) ◽

pp. 345a

Author(s):

Steffen Lindert ◽

Melanie Marlett

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Refinement ◽

Model Quality ◽

Protein Structure Refinement ◽

Protein Model

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Physics-based protein structure refinement through multiple molecular dynamics trajectories and structure averaging

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24336 ◽

2013 ◽

Vol 82 ◽

pp. 196-207 ◽

Cited By ~ 74

Author(s):

Vahid Mirjalili ◽

Keenan Noyes ◽

Michael Feig

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Refinement ◽

Protein Structure Refinement

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PREFMD: a web server for protein structure refinement via molecular dynamics simulations

Bioinformatics ◽

10.1093/bioinformatics/btx726 ◽

2017 ◽

Vol 34 (6) ◽

pp. 1063-1065 ◽

Cited By ~ 12

Author(s):

Lim Heo ◽

Michael Feig

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Structure Refinement ◽

Web Server ◽

Protein Structure Refinement ◽

Dynamics Simulations

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Local Protein Structure Refinement via Molecular Dynamics Simulations with locPREFMD

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.6b00222 ◽

2016 ◽

Vol 56 (7) ◽

pp. 1304-1312 ◽

Cited By ~ 23

Author(s):

Michael Feig

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Structure Refinement ◽

Protein Structure Refinement ◽

Local Protein Structure ◽

Dynamics Simulations ◽

Local Protein

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Protein Structure Refinement via Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2017.11.3143 ◽

2018 ◽

Vol 114 (3) ◽

pp. 575a ◽

Cited By ~ 2

Author(s):

Michael Feig ◽

Lim Heo

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Structure Refinement ◽

Protein Structure Refinement ◽

Dynamics Simulations

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Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles

Journal of Chemical Theory and Computation ◽

10.1021/ct300962x ◽

2013 ◽

Vol 9 (2) ◽

pp. 1294-1303 ◽

Cited By ~ 67

Author(s):

Vahid Mirjalili ◽

Michael Feig

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Refinement ◽

Structure Selection ◽

Protein Structure Refinement

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3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24167 ◽

2012 ◽

Vol 81 (1) ◽

pp. 119-131 ◽

Cited By ~ 97

Author(s):

Debswapna Bhattacharya ◽

Jianlin Cheng

Keyword(s):

Hydrogen Bonding ◽

Protein Structure ◽

Energy Minimization ◽

Structure Refinement ◽

Atomic Level ◽

Level Energy ◽

Protein Structure Refinement ◽

Hydrogen Bonding Network

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