Structure refinement of membrane proteins via molecular dynamics simulations

Bercem Dutagaci; Lim Heo; Michael Feig

doi:10.1002/prot.25508

Structure refinement of membrane proteins via molecular dynamics simulations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25508 ◽

2018 ◽

Vol 86 (7) ◽

pp. 738-750 ◽

Cited By ~ 5

Author(s):

Bercem Dutagaci ◽

Lim Heo ◽

Michael Feig

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Molecular Dynamics Simulations ◽

Structure Refinement ◽

Dynamics Simulations

Download Full-text

Faculty Opinions recommendation of Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model.

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

10.3410/f.1031397.363724 ◽

2006 ◽

Author(s):

D Peter Tieleman

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Molecular Dynamics Simulations ◽

Integral Membrane Proteins ◽

Membrane Model ◽

Dynamics Simulations

Download Full-text

Molecular Dynamics Simulations of Membrane Proteins

Methods in Molecular Biology - Membrane Biogenesis ◽

10.1007/978-1-62703-487-6_6 ◽

2013 ◽

pp. 85-101 ◽

Cited By ~ 11

Author(s):

Kristyna Pluhackova ◽

Tsjerk A. Wassenaar ◽

Rainer A. Böckmann

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations

Download Full-text

Chapter 7. Bridging the Gap Between Atomistic Molecular Dynamics Simulations and Wet-lab Experimental Techniques: Applications to Membrane Proteins

Theoretical and Computational Chemistry Series - Computational Techniques for Analytical Chemistry and Bioanalysis ◽

10.1039/9781788015882-00247 ◽

2020 ◽

pp. 247-286

Author(s):

Lucie Delemotte

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Molecular Dynamics Simulations ◽

Experimental Techniques ◽

Wet Lab ◽

Dynamics Simulations

Download Full-text

Folding and Assembly of Membrane Proteins: Coarse Grained Molecular Dynamics Simulations of EmrE

Biophysical Journal ◽

10.1016/j.bpj.2008.12.2843 ◽

2009 ◽

Vol 96 (3) ◽

pp. 379a

Author(s):

Kia Balali-mood ◽

Mark S.P. Sansom

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Molecular Dynamics Simulations ◽

Coarse Grained ◽

Dynamics Simulations ◽

Coarse Grained Molecular Dynamics

Download Full-text

Molecular Dynamics Simulations of Membrane Proteins

Methods in Molecular Biology - Molecular Modeling of Proteins ◽

10.1007/978-1-59745-177-2_8 ◽

2008 ◽

pp. 147-160 ◽

Cited By ~ 20

Author(s):

Philip C. Biggin ◽

Peter J. Bond

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations

Download Full-text

Integrating hydrogen–deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins

Nature Protocols ◽

10.1038/s41596-019-0219-6 ◽

2019 ◽

Vol 14 (11) ◽

pp. 3183-3204 ◽

Cited By ~ 10

Author(s):

Chloe Martens ◽

Mrinal Shekhar ◽

Andy M. Lau ◽

Emad Tajkhorshid ◽

Argyris Politis

Keyword(s):

Mass Spectrometry ◽

Molecular Dynamics ◽

Membrane Proteins ◽

Molecular Dynamics Simulations ◽

Conformational Changes ◽

Hydrogen Deuterium Exchange ◽

Exchange Mass Spectrometry ◽

Hydrogen Deuterium ◽

Deuterium Exchange Mass Spectrometry ◽

Dynamics Simulations

Download Full-text

Molecular dynamics simulations of membrane proteins

Biophysical Reviews ◽

10.1007/s12551-012-0084-9 ◽

2012 ◽

Vol 4 (3) ◽

pp. 271-282 ◽

Cited By ~ 8

Author(s):

Turgut Baştuğ ◽

Serdar Kuyucak

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations

Download Full-text

Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors

Current Opinion in Structural Biology ◽

10.1016/j.sbi.2011.06.008 ◽

2011 ◽

Vol 21 (4) ◽

pp. 552-558 ◽

Cited By ~ 56

Author(s):

Jennifer M Johnston ◽

Marta Filizola

Keyword(s):

Molecular Dynamics ◽

Membrane Proteins ◽

Molecular Dynamics Simulations ◽

G Protein ◽

G Protein Coupled Receptors ◽

Dynamics Simulations ◽

G Protein Coupled

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 ◽

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

Download Full-text

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 ◽

Molecular Dynamics Simulations ◽

Structure Refinement ◽

Langevin Dynamics ◽

Loop Conformations ◽

Dynamics Simulations

Download Full-text