Protein Structure Prediction Using an Associated Memory Hamiltonian and All-Atom Molecular Dynamics Simulations

Bulletin of the Korean Chemical Society ◽

10.5012/bkcs.2008.29.11.2172 ◽

2008 ◽

Vol 29 (11) ◽

pp. 2172-2182 ◽

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Dynamics Simulations

Download Full-text

Structural conversion of the transformer protein RfaH: new insights derived from protein structure prediction and molecular dynamics simulations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2014.994188 ◽

2015 ◽

Vol 33 (10) ◽

pp. 2173-2179 ◽

Author(s):

Nicole Balasco ◽

Daniela Barone ◽

Luigi Vitagliano

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Structural Conversion ◽

Dynamics Simulations

Download Full-text

Molecular dynamics simulations on protein folding and protein structure prediction

Journal of Molecular Graphics and Modelling ◽

10.1016/s1093-3263(00)80122-9 ◽

2000 ◽

Vol 18 (4-5) ◽

pp. 553

Author(s):

Peter Kollman

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Protein Structure Prediction ◽

Structure Prediction ◽

Dynamics Simulations

Download Full-text

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 ◽

Molecular Dynamics Simulations ◽

Structure And Dynamics ◽

Dynamics Simulations ◽

Partially Folded States ◽

Protein Structure And Dynamics

Download Full-text

De novo protein structure prediction using ultra-fast molecular dynamics simulation

PLoS ONE ◽

10.1371/journal.pone.0205819 ◽

2018 ◽

Vol 13 (11) ◽

pp. e0205819 ◽

Author(s):

Ngaam J. Cheung ◽

Wookyung Yu

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulation ◽

Protein Structure Prediction ◽

Structure Prediction ◽

De Novo ◽

Dynamics Simulation

Download Full-text

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 ◽

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

Download Full-text

Structure prediction and molecular dynamics simulations of a G-protein coupled receptor: human CCR2 receptor

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2012.707460 ◽

2013 ◽

Vol 31 (7) ◽

pp. 694-715 ◽

Author(s):

Rajesh Singh ◽

M. Elizabeth Sobhia

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

G Protein ◽

Structure Prediction ◽

G Protein Coupled Receptor ◽

Dynamics Simulations ◽

G Protein Coupled

Download Full-text

Thermostable chitinase II from Thermomyces lanuginosus SSBP: Cloning, structure prediction and molecular dynamics simulations

Journal of Theoretical Biology ◽

10.1016/j.jtbi.2015.03.035 ◽

2015 ◽

Vol 374 ◽

pp. 107-114 ◽

Author(s):

Faez Iqbal Khan ◽

Algasan Govender ◽

Kugen Permaul ◽

Suren Singh ◽

Krishna Bisetty

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Structure Prediction ◽

Thermomyces Lanuginosus ◽

Dynamics Simulations

Download Full-text

Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25079 ◽

2016 ◽

Vol 84 (9) ◽

pp. 1312-1320 ◽

Author(s):

Edoardo Sarti ◽

Ivan Gladich ◽

Stefano Zamuner ◽

Bruno E. Correia ◽

Alessandro Laio

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Protein Structure Prediction ◽

Structure Prediction

Download Full-text

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 ◽

Molecular Dynamics Simulations ◽

Replica Exchange ◽

Complex Type ◽

3D Protein Structure ◽

Replica Exchange Molecular Dynamics ◽

Biophysical Society ◽

Dynamics Simulations

Download Full-text

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 ◽

Author(s):

Michael Feig ◽

Vahid Mirjalili

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Structure Refinement ◽

Protein Structure Refinement ◽

Dynamics Simulations

Download Full-text