Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b03277 ◽

2018 ◽

Vol 122 (41) ◽

pp. 9435-9442 ◽

Author(s):

Wei Jiang ◽

Jonathan Thirman ◽

Sunhwan Jo ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

Dynamics Method

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A Refined Free Energy Perturbation Hamiltonian Replica Exchange Molecular Dynamics Method for Absolute Binding Affinity Predictions

Biophysical Journal ◽

10.1016/j.bpj.2017.11.3639 ◽

2018 ◽

Vol 114 (3) ◽

pp. 675a

Author(s):

Wei Jiang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Affinity ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Energy Perturbation ◽

Dynamics Method

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Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

Journal of Chemical Theory and Computation ◽

10.1021/ct1001768 ◽

2010 ◽

Vol 6 (9) ◽

pp. 2559-2565 ◽

Author(s):

Wei Jiang ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Faculty Opinions recommendation of Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

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

10.3410/f.718636459.8572054 ◽

2011 ◽

Author(s):

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Faculty Opinions recommendation of Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations.

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

10.3410/f.8162956.8572054 ◽

2011 ◽

Author(s):

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics

Journal of Chemical Theory and Computation ◽

10.1021/ct900223z ◽

2009 ◽

Vol 5 (10) ◽

pp. 2583-2588 ◽

Author(s):

Wei Jiang ◽

Milan Hodoscek ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Energy Perturbation

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Surface-Tension Replica-Exchange Molecular Dynamics Method for Efficient Conformational Sampling of Biological Membrane Systems

Biophysical Journal ◽

10.1016/j.bpj.2013.11.3894 ◽

2014 ◽

Vol 106 (2) ◽

pp. 704a ◽

Author(s):

Takaharu Mori ◽

Jaewoon Jung ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Surface Tension ◽

Biological Membrane ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Conformational Sampling ◽

Membrane Systems ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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Protein Folding with the Parallel Replica Exchange Molecular Dynamics Method

Parallel Computing for Bioinformatics and Computational Biology ◽

10.1002/0471756504.ch17 ◽

2005 ◽

pp. 395-425

Author(s):

Ruhong Zhou

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method

Journal of Computational Chemistry ◽

10.1002/jcc.24371 ◽

2016 ◽

Vol 37 (17) ◽

pp. 1565-1575 ◽

Author(s):

Changjun Chen ◽

Yanzhao Huang

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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Replica-exchange molecular dynamics method for protein folding

Chemical Physics Letters ◽

10.1016/s0009-2614(99)01123-9 ◽

1999 ◽

Vol 314 (1-2) ◽

pp. 141-151 ◽

Cited By ~ 2913

Author(s):

Yuji Sugita ◽

Yuko Okamoto

Keyword(s):

Molecular Dynamics ◽

Protein Folding ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Dynamics Method

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3PT157 Surface tension replica exchange molecular dynamics method for an efficient sampling of lipid bilayer structures(The 50th Annual Meeting of the Biophysical Society of Japan)

Seibutsu Butsuri ◽

10.2142/biophys.52.s168_1 ◽

2012 ◽

Vol 52 (supplement) ◽

pp. S168

Author(s):

Takaharu Mori ◽

Yuji Sugita

Keyword(s):

Molecular Dynamics ◽

Surface Tension ◽

Annual Meeting ◽

Lipid Bilayer ◽

Molecular Dynamics Method ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Efficient Sampling ◽

Biophysical Society ◽

Dynamics Method

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