For DOCK 6, both the ligand and the receptor files were prepared in Tripos mol2 format using Chimera. Partial charges were added to the atoms using AM1-BCC method within Chimera. Next, we generated a molecular surface for the receptors without the hydrogen atoms using the dms functionality in Chimera, followed by the creation of the docking spheres using the sphgen program within DOCK 6. A subset of the spheres which were within 7 Å of the binding site (Fig. ) were selected using the accessory program sphere_selector. Then, we created a box around the spheres with a margin of 5 Å using the program showbox in the DOCK suite. Next, the energy interactions were evaluated between a dummy atom and all protein atoms within 0.3 Å resolution using the DOCK accessory program GRID . Van der Waals interactions were modeled using 6-12 Lennard-Jones potential and electrostatic interactions using Coulomb potential with a dielectric coefficient of ε=4r, where r is the distance. The resulting grid was used to score the binding poses using grid-score . For the docking algorithm, we used standard parameters mentioned by Allen et al. .