To sum up, we used ligand similarity to predict binding conformations for the cross-docking and self-docking challenge and MM-GBSA scores to rank ligand affinities. Our ligand similarity-based protocol was able to identify binding poses close to the native poses with an accuracy of 2 Å for most of the ligands. On the other hand, our predicted MM-GBSA scores had a weak correlation with the experimental affinities.