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ensemble simulation

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5 results in Keywords: ensemble simulation

Theoretical and Computational Chemistry

Extending the MMPBSA method to membrane proteins: Addressing conformational changes upon ligand binding to P2Y12R

Cizhang Zhao, Tianhong Wang, Ray Luo

Version 2 posted 04 April 2025

166

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Theoretical and Computational Chemistry

Non-Gaussian distributions of absolute free energies in ensemble molecular dynamics simulations

Peter Coveney, Shunzhou Wan

Version 2 posted 25 July 2023

272

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1

Citations

Theoretical and Computational Chemistry

Which corners to cut? Guidelines on choosing optimal settings to maximise sampling with limited computational resources

Peter V. Coveney, Shunzhou Wan, Agastya P. Bhati, Alexander D. Wade

Version 1 posted 05 August 2022

224

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2

Citations

Theoretical and Computational Chemistry

Large Scale Study of Ligand-Protein Relative Binding Free Energy Calculations: Actionable Predictions from Statistically Robust Protocols

Agastya P Bhati, Peter V. Coveney

Version 2 posted 02 March 2022

587

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Theoretical and Computational Chemistry

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Shunzhou Wan, Agastya P. Bhati, David W. Wright, Alexander D. Wade, Gary Tresadern, Herman van Vlijmen, Peter V. Coveney

Version 1 posted 14 March 2022

221

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