Figure 2 | Scientific Reports

Figure 2

From: Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A 2A adenosine receptor binding site

Figure 2

Thermodynamic cycle used to calculate relative free energies of binding (ΔΔGbind) from MD simulations. Alchemical transformations of the ligands L and L’ were performed in aqueous solution (ΔGaq, left panel) and bound to the receptor (ΔGprot, right panel). The protein is shown as green cartoon and the ligand is depicted in sticks. Water molecules are shown as red spheres and membrane carbon atoms are represented by grey spheres.

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