Figure 2.

Overview of the computational procedure. In the first step, a homology model of Kv1.5 (cyan) is constructed using a template structure (orange). An octane membrane model (yellow) is then built around the ion channel and the system is equilibrated in water. In the next step, the water molecules are removed and automated docking is used to fit the ligands (purple) into the pore cavity. Finally, the complexes are solvated again for refinement and free energy calculations by molecular dynamics simulations, utilizing more efficient reduced spherical systems.