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

Structure Refinement ◽

What Works ◽

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 ◽

Structure Refinement ◽

Experimental Accuracy ◽

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 ◽

Structure Refinement ◽

Web Server ◽

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 ◽

Structure Refinement ◽

Local Protein Structure ◽

Dynamics Simulations ◽

Local Protein

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 ◽

Structure Refinement ◽

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.734614719.793558412 ◽

2019 ◽

Author(s):

Patrice Koehl

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Refinement ◽

Experimental Accuracy ◽

Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21674 ◽

2007 ◽

Vol 70 (4) ◽

pp. 1345-1356 ◽

Cited By ~ 31

Author(s):

Andrew W. Stumpff-Kane ◽

Katarzyna Maksimiak ◽

Michael S. Lee ◽

Michael Feig

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Refinement ◽

Normal Modes ◽

Coarse Grained ◽

Protein Conformations ◽

Native Protein ◽

Coarse Grained Model ◽

Faculty Opinions recommendation of Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics.

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

10.3410/f.1088149.542736 ◽

2007 ◽

Author(s):

Bernard Montgomery Pettitt

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure And Dynamics ◽

Dynamics Simulations ◽

Partially Folded States ◽

Protein Structure And Dynamics

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

3D0936 Prediction of dynamical conformation of biantennary complex-type N-glycan in water by replica-exchange molecular dynamics simulations(3D Protein: Structure & Function 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.51.s117_3 ◽

2011 ◽

Vol 51 (supplement) ◽

pp. S117

Author(s):

Suyong Re ◽

Naoyuki Miyashita ◽

Yoshiki Yamaguchi ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Structure Function ◽

Replica Exchange ◽

Complex Type ◽

3D Protein Structure ◽

Replica Exchange Molecular Dynamics ◽

Biophysical Society ◽

Comparison between self-guided Langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations

Journal of Computational Chemistry ◽

10.1002/jcc.21883 ◽

2011 ◽

Vol 32 (14) ◽

pp. 3014-3022 ◽

Cited By ~ 22

Author(s):

Mark A. Olson ◽

Sidhartha Chaudhury ◽

Michael S. Lee

Keyword(s):

Molecular Dynamics ◽

Structure Refinement ◽

Langevin Dynamics ◽

Loop Conformations ◽