Constrained molecular dynamics in the isothermal-isobaric ensemble and its adaptation for adiabatic free energy dynamics

2011 ◽  
Vol 200 (1) ◽  
pp. 183-209 ◽  
Author(s):  
T. -Q. Yu ◽  
M. E. Tuckerman
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Dynamics

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

A molecular dynamics study on liquid 1-octanol. Part 3. Evaluating octanol/water partition coefficients of novel thrombin inhibitors via free-energy perturbations

2005 ◽  
Vol 102 (5) ◽  
pp. 542-553 ◽  
Author(s):  
César Augusto Fernandes De Oliveira ◽  
Cristiano Ruch Werneck Guimarães ◽  
Heloisa De Mello ◽  
Aurea Echevarria ◽  
Ricardo Bicca De Alencastro
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Partition Coefficients ◽  
Thrombin Inhibitors ◽  
Free Energy Perturbations

scholarly journals Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges

2021 ◽  
Author(s):  
Lorenzo Casbarra ◽  
Piero Procacci
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Drug Discovery ◽  
Binding Free Energy ◽  
Cost Ratio ◽  
Benefit Cost Ratio ◽  
Docking Program ◽  
Benefit Cost ◽  
Overall Reliability ◽  
Absolute Binding Free Energy

AbstractWe systematically tested the Autodock4 docking program for absolute binding free energy predictions using the host-guest systems from the recent SAMPL6, SAMPL7 and SAMPL8 challenges. We found that Autodock4 behaves surprisingly well, outperforming in many instances expensive molecular dynamics or quantum chemistry techniques, with an extremely favorable benefit-cost ratio. Some interesting features of Autodock4 predictions are revealed, yielding valuable hints on the overall reliability of docking screening campaigns in drug discovery projects.

Steric and Electrostatic Effects on the Diffusion of CH4/CH3OH in Copper-Exchanged Zeolites: Insights from Enhanced Sampling Molecular Dynamics and Free Energy Calculations

Langmuir ◽  
2021 ◽  
Author(s):  
Luis Paulo M. Freitas ◽  
Anderson A. Espírito Santo ◽  
Tuanan C. Lourenço ◽  
Juarez L. F. Da Silva ◽  
Gustavo Troiano Feliciano
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Free Energy Calculations ◽  
Enhanced Sampling ◽  
Electrostatic Effects ◽  
Energy Calculations
Sign in / Sign up

Export Citation Format

Share Document