Fig. 3: Comparison of experimentally measured and calculated binding affinities for TNKS2 protein-ligand system.
From: Automated relative binding free energy calculations from SMILES to ΔΔG
The simulations were initialized with different starting structures (docked/modelled or docked only). The data in the panel Docked/modelled FEP+ are from Schindler et al.4. The data in the panel Docked/modelled PMX/GAFF are from Gapsys et al.13. Overlays of starting ligand poses are inset into the corresponding plot. Experimental errors are taken from the original publication, whilst prediction errors correspond to the standard error over 3 simulation replicas also taking into account the bootstrapped uncertainty of individual free energy estimates. The shaded grey region corresponds to a 1 kcal mol−1 deviation from experiment, and the solid line is a linear fit through the data. The crystal structure with a bound ligand highlighted in orange is shown in the top right.
