A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories

Daria B. Kokh; Bernd Doser; Stefan Richter; Fabian Ormersbach; Xingyi Cheng; Rebecca C. Wade

doi:10.1063/5.0019088

A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories

The Journal of Chemical Physics ◽

10.1063/5.0019088 ◽

2020 ◽

Vol 153 (12) ◽

pp. 125102

Author(s):

Daria B. Kokh ◽

Bernd Doser ◽

Stefan Richter ◽

Fabian Ormersbach ◽

Xingyi Cheng ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Fingerprint Analysis ◽

Ligand Dissociation ◽

Random Acceleration ◽

Random Acceleration Molecular Dynamics

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Exploring ligand dissociation pathways from aminopeptidase N using random acceleration molecular dynamics simulation

Journal of Molecular Modeling ◽

10.1007/s00894-016-3105-y ◽

2016 ◽

Vol 22 (10) ◽

Cited By ~ 1

Author(s):

Ya Liu ◽

GuoGang Tu ◽

XiaoPing Lai ◽

BinHai Kuang ◽

ShaoHua Li

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Aminopeptidase N ◽

Dynamics Simulation ◽

Ligand Dissociation ◽

Random Acceleration ◽

Random Acceleration Molecular Dynamics

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Unraveling the Unbinding Pathways of Products Formed in Catalytic Reactions Involved in SIRT1–3: A Random Acceleration Molecular Dynamics Simulation Study

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.9b00513 ◽

2019 ◽

Vol 59 (10) ◽

pp. 4100-4115 ◽

Cited By ~ 2

Author(s):

Charuvaka Muvva ◽

N. Arul Murugan ◽

Venkata Surya Kumar Choutipalli ◽

Venkatesan Subramanian

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Catalytic Reactions ◽

Dynamics Simulation ◽

Random Acceleration ◽

Random Acceleration Molecular Dynamics

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Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.90.12.5805 ◽

1993 ◽

Vol 90 (12) ◽

pp. 5805-5807 ◽

Cited By ~ 45

Author(s):

K. Kuczera ◽

J. C. Lambry ◽

J. L. Martin ◽

M. Karplus

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Ligand Dissociation

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Case Study on Temperature-Accelerated Molecular Dynamics Simulation of Ligand Dissociation: Inducer Dissociation from the Lac Repressor Protein

The Journal of Physical Chemistry A ◽

10.1021/jp503856h ◽

2014 ◽

Vol 118 (39) ◽

pp. 9272-9279 ◽

Cited By ~ 5

Author(s):

Yue Hu ◽

Haiyan Liu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Lac Repressor ◽

Dynamics Simulation ◽

Repressor Protein ◽

Ligand Dissociation ◽

Accelerated Molecular Dynamics

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Molecular Dynamics Simulation of Ligand Dissociation from Liver Fatty Acid Binding Protein

PLoS ONE ◽

10.1371/journal.pone.0006081 ◽

2009 ◽

Vol 4 (6) ◽

pp. e6081 ◽

Cited By ~ 42

Author(s):

Dong Long ◽

Yuguang Mu ◽

Daiwen Yang

Keyword(s):

Molecular Dynamics ◽

Fatty Acid ◽

Molecular Dynamics Simulation ◽

Fatty Acid Binding Protein ◽

Binding Protein ◽

Dynamics Simulation ◽

Liver Fatty Acid ◽

Fatty Acid Binding ◽

Ligand Dissociation ◽

Acid Binding Protein

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1P044 Ligand-dissociation increases protein flexibility in trp RNA-binding attenuation protein (TRAP) : Molecular dynamics simulation study(1. Protein structure and dynamics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s157_4 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S157

Author(s):

Hidemi Araki ◽

Sotaro Fuchigami ◽

Mitsunori Ikeguchi ◽

Jonathan G. Heddle ◽

Jeremy R. H. Tame ◽

...

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulation ◽

Poster Session ◽

Rna Binding ◽

Dynamics Simulation ◽

Ligand Dissociation ◽

Structure And Dynamics ◽

Meeting Program ◽

Protein Structure And Dynamics

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Rotational dynamics and velocity segregation in plastic KCIO4: a molecular dynamics simulation

Molecular Physics ◽

10.1080/00268979809482256 ◽

1998 ◽

Vol 93 (5) ◽

pp. 703-711

Author(s):

F. AFFOUARD ◽

PH. DEPONDT

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Rotational Dynamics ◽

Dynamics Simulation

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Molecular dynamics simulation of the dynamics of supercooled silica

Philosophical Magazine B ◽

10.1080/014186398259374 ◽

1998 ◽

Vol 77 (2) ◽

pp. 297-303 ◽

Cited By ~ 24

Author(s):

J. Horbach, W. Kob, K. Binder

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation

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ACPD ligands for glutamic receptors : conformational analysis by NMR spectroscopy and molecular dynamics. Simulation in water of glutamic acid analogues containing a cyclopentane ring

Journal de Chimie Physique ◽

10.1051/jcp/1995921809 ◽

1995 ◽

Vol 92 ◽

pp. 1809-1812

Author(s):

V Larue ◽

J Gharby-Benarous ◽

D Todeschi ◽

F Acher ◽

R Azerad ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Nmr Spectroscopy ◽

Conformational Analysis ◽

Glutamic Acid ◽

Dynamics Simulation ◽

Cyclopentane Ring

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Nonequilibrium effects in electron-ion strongly coupled plasmas. Molecular dynamics simulation

Journal de Physique IV (Proceedings) ◽

10.1051/jp4:2000545 ◽

2000 ◽

Vol 10 (PR5) ◽

pp. Pr5-255-Pr5-258 ◽

Cited By ~ 5

Author(s):

G. E. Norman ◽

A. A. Valuev ◽

I. A. Valuev

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Strongly Coupled ◽

Strongly Coupled Plasmas ◽

Nonequilibrium Effects ◽

Coupled Plasmas

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