3D-Shape analysis of the HIV-1 protease ligand binding site

Using a shape analysis technique, a dataset of 83 (20 wild-type and 63 mutated) HIV-1 protease crystal structures is analyzed for the shape changes in their binding pockets. The structures were reported with different bound inhibitors (ligands) and consist of a variety of mutations. Several geometrical and topological attributes based on the volumetric shape function and few other additional properties like electrostatic potential function were calculated. A cluster analysis was performed using these calculated attributes to investigate the effect of mutations or ligand on the shape change of the binding pocket of HIV protease.