The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals.
Cho AE, Wendel JA, Vaidehi N, Kekenes-Huskey PM, Floriano WB, Maiti PK, Goddard WA 3rd, J Comput Chem, 2005 Jan 15 - link

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.
Floriano WB, Vaidehi N, Zamanakos G, Goddard WA 3rd, J Med Chem, 2004 Jan 1 - link