Figure 2.

Progression of the number of water molecules in the Gleevec-binding pockets of Abl, c-Kit, Lck, and c-Src in response to binding during the FEP calculations. The simulations are divided into 31 stages, starting from repulsive stage 1 and progressing to fully interacting ligand in stage 31. In stages 1–9, the ligand repulsion is gradually switched on. In stages 10–20, the ligand dispersion is turned on. In the stages 21–31, the charges of the ligand are added progressively.