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Application of ESMACS Binding Free Energy Protocols to Diverse Datasets: Bromodomain-Containing Protein 4

04 March 2019, Version 2
Working Paper
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

We investigate the robustness of our ensemble molecular dynamics binding free energy protocols, known as ESMACS, to different choices of forcefield, starting structure and analysis. ESMACS is based on MMPBSA and we examinge the influence of multiple trajectories, explicit water molecules and estimates of the entropic contribution to the binding free energy.

Simulation input and binding affinity calculation data:
https://doi.org/10.5281/zenodo.1484050

Keywords

Molecular dynamics
MMPBSA
Binding Free Energy Estimation

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Now Published

Application of ESMACS binding free energy protocols to diverse datasets: Bromodomain-containing protein 4 [opens in a new tab]
David W. Wright, Shunzhou Wan, Christophe Meyer, Herman van Vlijmen, Gary Tresadern, Peter V. Coveney journal article
Scientific Reports , Volume 9, Issue 1
Online publication date: Apr 12, 2019

Version History

Mar 04, 2019 Version 2

Version Notes

Post first review edits

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The content is available under CC BY 4.0 [opens in a new tab]

DOI

10.26434/chemrxiv.7327019.v2
D O I: 10.26434/chemrxiv.7327019.v2 [opens in a new tab]

Funding

ComPat (EU H2020: 671564)
CompBioMed (EU H2020: 67545)
VECMA (EU H2020: 800925)
INSPIRE (US DoE: DE-AC05-00OR22725)

Author’s competing interest statement

No conflict of interest

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