Figure 3
New method for determining the optimal separation between the interacting molecules, for each sampled orientation. (A) A triangular grid (orthogonal to the direction of the interaction v r ) is used to generate a 2 D projection of the receptor (in blue ribbon) surface, by computing the distance from each grid point to the furthest surface backbone atoms (grey spheres). B) The grid points are shown here coloured according to the distance to the surface backbone atoms from black to red (red indicates maximum distance to the surface). C) This process is repeated for the ligand molecule, and the two grids are summed up. The value of the maximum element of the sum matrix (plus some fixed extra space ϵ to account for the volume of the side chains) will define the final separation distance r between the centers of mass of the molecules.