Biological and Medicinal Chemistry

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

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

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