scholarly journals Predicting gas selectivity in organic ionic plastic crystals by free energy calculations

RSC Advances ◽  
2021 ◽  
Vol 11 (32) ◽  
pp. 19623-19629
Author(s):  
Vinay S. Kandagal ◽  
Jennifer M. Pringle ◽  
Maria Forsyth ◽  
Fangfang Chen
Keyword(s):  
Free Energy ◽  
Gas Separation ◽  
Free Energy Calculations ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Plastic Crystal ◽  
Plastic Crystals ◽  
New Type ◽  
Gas Molecules ◽  
Gas Selectivity

The free energy calculation shows the different free energy changes of the adsorption and absorption of gas molecules into an organic ionic plastic crystal, successfully predicting the gas selectivity of this new type of gas separation material.

scholarly journals Implementation of the QUBE Force Field for High-Throughput Alchemical Free Energy Calculations

2020 ◽  
Author(s):  
Lauren Nelson ◽  
Sofia Bariami ◽  
Chris Ringrose ◽  
Joshua Horton ◽  
Vadiraj Kurdekar ◽  
...  
Keyword(s):  
Free Energy ◽  
Force Field ◽  
High Throughput ◽  
Potential Energy Function ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Alchemical Free Energy ◽  
Simulation Package

<div><div><div><p>The quantum mechanical bespoke (QUBE) force field approach has been developed to facilitate the automated derivation of potential energy function parameters for modelling protein-ligand binding. To date the approach has been validated in the context of Monte Carlo simulations of protein-ligand complexes. We describe here the implementation of the QUBE force field in the alchemical free energy calculation molecular dynamics simulation package SOMD. The implementation is validated by computing relative binding free energies for two congeneric series of non-nucleoside inhibitors of HIV-1 reverse transcriptase using QUBE and AMBER/GAFF force fields. The availability of QUBE in a modern simulation package that makes efficient use of GPU acceleration will greatly facilitate future high-throughput alchemical free energy calculation studies.</p></div></div></div>

Insights into the effects of mutations on Cren7–DNA binding using molecular dynamics simulations and free energy calculations

2015 ◽  
Vol 17 (8) ◽  
pp. 5704-5711 ◽  
Author(s):  
Lin Chen ◽  
Qing-Chuan Zheng ◽  
Hong-Xing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Free Energy Calculations ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Dynamic Effects ◽  
Cellular Processes ◽  
Dynamics Simulations

Cren7 is involved in regulating essential cellular processes. We applied MD simulations and free energy calculation to explore the structural and dynamic effects of W26A, L28A, and K53A mutations.

scholarly journals Implementation of the QUBE Force Field for High-Throughput Alchemical Free Energy Calculations

2020 ◽  
Author(s):  
Lauren Nelson ◽  
Sofia Bariami ◽  
Chris Ringrose ◽  
Joshua Horton ◽  
Vadiraj Kurdekar ◽  
...  
Keyword(s):  
Free Energy ◽  
Force Field ◽  
High Throughput ◽  
Potential Energy Function ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Alchemical Free Energy ◽  
Simulation Package

<div><div><div><p>The quantum mechanical bespoke (QUBE) force field approach has been developed to facilitate the automated derivation of potential energy function parameters for modelling protein-ligand binding. To date the approach has been validated in the context of Monte Carlo simulations of protein-ligand complexes. We describe here the implementation of the QUBE force field in the alchemical free energy calculation molecular dynamics simulation package SOMD. The implementation is validated by computing relative binding free energies for two congeneric series of non-nucleoside inhibitors of HIV-1 reverse transcriptase using QUBE and AMBER/GAFF force fields. The availability of QUBE in a modern simulation package that makes efficient use of GPU acceleration will greatly facilitate future high-throughput alchemical free energy calculation studies.</p></div></div></div>

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects

2020 ◽  
Author(s):  
Christina Schindler ◽  
Hannah Baumann ◽  
Andreas Blum ◽  
Dietrich Böse ◽  
Hans-Peter Buchstaller ◽  
...  
Keyword(s):  
Free Energy ◽  
Drug Discovery ◽  
Large Scale ◽  
Active Drug ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculation ◽  
Large Scale Assessment ◽  
New Public ◽  
Binding Free Energy Calculations

Here we present an evaluation of the binding affinity prediction accuracy of the free energy calculation method FEP+ on internal active drug discovery projects and on a large new public benchmark set.<br>

Free Energy Calculation Methods of Biomolecules

2011 ◽  
Vol 27 (5) ◽  
pp. 395-402 ◽  
Author(s):  
Changjun CHEN ◽  
Yanzhao HUANG ◽  
Yi XIAO
Keyword(s):  
Free Energy ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Calculation Methods
Sign in / Sign up

Export Citation Format

Share Document