Identifying Ligand Binding Sites and Poses Using GPU-accelerated Hamiltonian Replica Exchange Molecular Dynamics

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-013-9689-8 ◽

2013 ◽

Vol 27 (12) ◽

pp. 989-1007 ◽

Cited By ~ 78

Author(s):

Kai Wang ◽

John D. Chodera ◽

Yanzhi Yang ◽

Michael R. Shirts

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Binding Sites ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Ligand Binding Sites

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Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach

The Journal of Chemical Physics ◽

10.1063/1.3086832 ◽

2009 ◽

Vol 130 (10) ◽

pp. 104110 ◽

Cited By ~ 34

Author(s):

Jeremy Curuksu ◽

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Nucleic Acids ◽

Replica Exchange ◽

Conformational Sampling ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange

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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 ◽

Cited By ~ 16

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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Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics

Journal of Chemical Theory and Computation ◽

10.1021/ct501034w ◽

2015 ◽

Vol 11 (5) ◽

pp. 2234-2244 ◽

Cited By ~ 10

Author(s):

Sunhwan Jo ◽

Christophe Chipot ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Relative Entropy ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange

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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 ◽

Cited By ~ 159

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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Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: Application in the refinement of de novo models

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24068 ◽

2012 ◽

Vol 80 (7) ◽

pp. 1744-1754 ◽

Cited By ~ 10

Author(s):

Hao Fan ◽

Xavier Periole ◽

Alan E. Mark

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

De Novo ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Dynamics Simulations

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Predicting lipid and ligand binding sites in TRPV1 channel by molecular dynamics simulation and machine learning

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.26075 ◽

2021 ◽

Author(s):

Wenjun Zheng ◽

Han Wen

Keyword(s):

Machine Learning ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Ligand Binding ◽

Binding Sites ◽

Dynamics Simulation ◽

Trpv1 Channel ◽

Ligand Binding Sites

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Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct200153u ◽

2011 ◽

Vol 7 (9) ◽

pp. 2721-2727 ◽

Cited By ~ 44

Author(s):

Yilin Meng ◽

Danial Sabri Dashti ◽

Adrian E. Roitberg

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Replica Exchange ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Alchemical Free Energy

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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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