The molecular mechanism of ligand unbinding from the human telomeric G-quadruplex by steered molecular dynamics and umbrella sampling simulations

2015 ◽  
Vol 17 (19) ◽  
pp. 12857-12869 ◽  
Author(s):  
Jia-Kai Zhou ◽  
Dah-Yen Yang ◽  
Sheh-Yi Sheu
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Mechanism ◽  
Steered Molecular Dynamics ◽  
Umbrella Sampling ◽  
Energy Profiles ◽  
G Quadruplex ◽  
Free Energy Profiles

The mechanical properties and kinetic pathways of the ligand BMVC unbinding from the G-quadruplex were investigated via the computation of free energy profiles.

Displacement of carbonates in Ca2UO2(CO3)3 by amidoxime-based ligands from free-energy simulations

2018 ◽  
Vol 47 (5) ◽  
pp. 1604-1613 ◽  
Author(s):  
Bo Li ◽  
Chad Priest ◽  
De-en Jiang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Umbrella Sampling ◽  
Nacl Solution ◽  
Classical Molecular Dynamics ◽  
Energy Profiles ◽  
Energy Simulations ◽  
Dynamics Simulations ◽  
Free Energy Profiles

Classical molecular dynamics simulations coupled with umbrella sampling reveal the atomistic processes and free-energy profiles of the displacement of carbonate groups in the Ca2UO2(CO3)3 complex by amidoxime-based ligands in a 0.5 M NaCl solution.

scholarly journals Comparison of Umbrella Sampling and Steered Molecular Dynamics Methods for Computing Free Energy Profiles of Toluene Molecules through Phospholipid Bilayers

2019 ◽  
Author(s):  
Sang Noh ◽  
Rebecca Notman
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Computational Efficiency ◽  
Steered Molecular Dynamics ◽  
Umbrella Sampling ◽  
Energy Profiles ◽  
Toluene Molecule ◽  
Molecular Dynamics Methods ◽  
Viable Approach ◽  
The Cost

In this study, we use Molecular Dynamics (MD) to analyze three different corrections of the Steered Molecular Dynamics (SMD) implementation of Jarzynski's Equality (JE) to calculate the FE change for the translocation of a toluene molecule across a lipid bilayer, and compare the accuracy and computational efficiency of these approaches to the results obtained using Umbrella Sampling (US). We show that when computing the free energy profile of a small molecule across a model membrane, the SMD approach suffers from sampling issues that may be alleviated through the use of a slower pulling velocity, but at the cost of computational efficiency. We deduce that, despite its drawbacks, US remains the more viable approach of the two for computing the free energy (FE) profile.

scholarly journals Comparison of Umbrella Sampling and Steered Molecular Dynamics Methods for Computing Free Energy Profiles of Toluene Molecules through Phospholipid Bilayers

2019 ◽  
Author(s):  
Sang Noh ◽  
Rebecca Notman
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Computational Efficiency ◽  
Steered Molecular Dynamics ◽  
Umbrella Sampling ◽  
Energy Profiles ◽  
Toluene Molecule ◽  
Molecular Dynamics Methods ◽  
Viable Approach ◽  
The Cost

In this study, we use Molecular Dynamics (MD) to analyze three different corrections of the Steered Molecular Dynamics (SMD) implementation of Jarzynski's Equality (JE) to calculate the FE change for the translocation of a toluene molecule across a lipid bilayer, and compare the accuracy and computational efficiency of these approaches to the results obtained using Umbrella Sampling (US). We show that when computing the free energy profile of a small molecule across a model membrane, the SMD approach suffers from sampling issues that may be alleviated through the use of a slower pulling velocity, but at the cost of computational efficiency. We deduce that, despite its drawbacks, US remains the more viable approach of the two for computing the free energy (FE) profile.

On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles

2002 ◽  
Vol 116 (11) ◽  
pp. 4389-4402 ◽  
Author(s):  
Lula Rosso ◽  
Peter Mináry ◽  
Zhongwei Zhu ◽  
Mark E. Tuckerman
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Profiles ◽  
Free Energy Profiles

Energetics of nonpolar and polar compounds in cationic, anionic, and nonionic micelles studied by all-atom molecular dynamics simulation combined with a theory of solutions

2016 ◽  
Vol 18 (19) ◽  
pp. 13223-13231 ◽  
Author(s):  
Atsushi Date ◽  
Ryosuke Ishizuka ◽  
Nobuyuki Matubayasi
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Polar Compounds ◽  
Dynamics Simulation ◽  
Energy Profiles ◽  
Polar Solutes ◽  
Free Energy Profiles

Free-energy profiles of binding nonpolar and polar solutes in cationic, anionic, and nonionic micelles.

Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics

2020 ◽  
Vol 22 (37) ◽  
pp. 21238-21250
Author(s):  
Jianzhong Chen ◽  
Wei Wang ◽  
Laixue Pang ◽  
Weiliang Zhu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Conformational Dynamics ◽  
Conformational Transformation ◽  
Accelerated Molecular Dynamics ◽  
Energy Profiles ◽  
Free Energy Profiles

The conformational transformation of two switches caused by mutations induces different free energy profiles of H-Ras.

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