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SciRep_BRD4_ESMACS.pdf (3.79 MB)
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Application of ESMACS Binding Free Energy Protocols to Diverse Datasets: Bromodomain-Containing Protein 4

preprint
revised on 04.03.2019 and posted on 04.03.2019 by David Wright, Shunzhou Wan, Christophe Meyer, Herman Van Vlijmen, Gary Tresadern, Peter Coveney
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

Funding

ComPat (EU H2020: 671564)

CompBioMed (EU H2020: 67545)

VECMA (EU H2020: 800925)

INSPIRE (US DoE: DE-AC05-00OR22725)

History

Email Address of Submitting Author

dave.wright@ucl.ac.uk

Institution

University College London

Country

United Kingdom

ORCID For Submitting Author

0000-0002-5124-8044

Declaration of Conflict of Interest

No conflict of interest

Version Notes

Post first review edits

Licence

Exports