In Stage 1a of D3R GC4, the participants were asked to predict the binding affinities of 154 BACE-1 compounds using any available PDB structure data or binding data. At the end of Stage 1, co-crystal structures of additional 20 ligands were released by the D3R organizers, allowing the participants to use these structures to refine the affinity predictions. In the present work, we describe our participation in Stage 2, where we predicted the binding affinities of the 154 ligands.