To evaluate this, we selected three targets with multiple ligand co-complexes from the same set of experiments: one determined with x-ray crystallography and two with cryo-EM. The Anaplastic Lymphoma Kinase (ALK) was selected as the x-ray crystallography target. The initial hit Crizotinib (PF-2341066) was further developed into a macrocyclic series containing Lorlatinib (PF-06463922) , for which several co-crystal structures were determined. This dataset contains 7 receptor structures and 11 ligands. 7 ligands were present as co-crystallized molecules in the target structures, while the remaining 4 were added as known and clinically-relevant tyrosine kinase inhibitors (TKIs). The µ opioid receptor (µOR) was chosen as a cryo-EM target of interest. The selected ligands and receptor structures were determined by Zhuang et al. as part of a study examining how the different binding modes of µOR agonists lead to distinct signaling activity. The µOR ligands display a diverse set of binding modes involving multiple subpockets, presenting a challenging case with a poorly-defined common pharmacophore. Finally, the HIV intasome was also selected as a cryo-EM target featuring a complex binding environment. HIV intasome is comprised of the viral HIV integrase protein and the viral DNA, and represents the complex before insertion of the viral DNA into the host genome. The binding site sits at the protein-nucleic acid interface and is further complicated by the presence of two magnesium cations which are coordinated by known active-site integrase inhibitors. This dataset contains 4 receptor holo structure and 7 total ligands after the addition of 3 clinical integrase inhibitors. The chemical structures for all docked ligands in this dataset are shown in Figure . A summary of all associated PDB and ligands IDs may be found in Supplementary Table . For all three targets, we evaluated two different methods for using the available density information. In the first scheme, we applied guidance using only the matching density for each holo receptor ("matched density guidance"). That is, when docking into the ALK receptor structure 4CLI, only the density for the ligand resolved in the structure 4CLI (Lorlatinib) was used as guidance. The second scheme is what we have called "consensus density guidance", in which (1) the density of each holo complex for a given target was normalized independently, then (2) the densities were aligned to the docking target structure and combined at each grid point to generate an averaged density map. The results for docking ALK ligands with the standard docking protocol (no guidance), the guidance from the density map corresponding to the individual receptor complex, or the guidance from a consensus density are shown in Figure . For the first seven tested ALK ligands, the unguided success rate (docking pose < 2Å RMSD from crystallographic pose) in re-docking was 5/7 (71%, denoted by black outline in Fig. ), while cross-docking success is slightly lower at 29/42 (69%). Guidance based on the density matched to each receptor structure improved both cross-docking (39/42, 93%) and re-docking (7/7, 100%). Averaging the density from the multiple ligands improves cross-docking success even further (42/42, 100%). The TKI cross-dockings perform worse, with only Ceritinib consistently exhibiting successful dockings with RMSD < 2Å (Fig. ). Comparisons of the docked poses with the reference poses reveal clear structural reasons for these discrepancies. The Alectinib reference pose is shown to have a clash with the residue Leu1196 in the holo structures used in this experiment (Fig. ), resulting in a 180°rotation in the docking pose. Notably, this pose retains the placement of the important ketone hydrogen bond acceptor. Brigatinib (Fig. ) and Ceritinib (Fig. ) cross-dockings suffer from similar errors in the placement of distal groups. The consensus density guidance forces the aniline into a position matching the input density but not the ligand to be docked, illustrating how for optimal performance, shape and location of the density used for the guidance should not be too different from the ligand to be docked and compatible with its ideal binding mode. Importantly, the common kinasebinding pharmacophores are still correctly positioned. In order to investigate the impact of the resolution of the input structural density, we used the Relion software to low-pass filter the deposited densities to resolutions of 3 Å, 4 Å, and 5 Å. The resulting re-docking and cross-docking RMSDs with the consensus density guidance derived from these degraded densities is shown in Figure . As expected, re-docking and cross-docking accuracy for the ligands whose densities were used to derived the guidance decreases slightly, but remains below 2 Å RMSD for all dockings with 3 Å and 4 Å resolution maps. Meanwhile, the crossdocking accuracy of Crizotinib improved with the degraded 3 Å and 4 Å resolution maps. Ligands for µOR share a less well-defined common pharmacophore than seen previously with ALK, resulting in a more challenging docking task even with density guidance. RMSD results for µOR are shown in Figure . Default AutoDock-GPU fails to predict correct binding poses for nearly every re-docking (1/6, 17%) and cross-docking (1/30, 3%). Redocking performs best with matching density guidance (4/6, 67%), with the challenging DAMGO peptide being docked successfully. Cross-docking was more successful with consensus density guidance (8/30, 27%). As shown in Figure , docking fentanyl with the consensus density guidance correctly positions the phenylethyl ring in the minor pocket between TM2 and TM3, but switches the position of the aniline ring and propylamide chain within the main pocket. Docking DAMGO (Fig. ) also positions aromatic rings in pharmacophorically-correct locations in the main and TM2/TM3 pockets, but switches the tyrosine and phenylalanine side chains and misorients the tyrosine in the TM2/TM3 pocket. Finally, SR17018 is docked in a reversed binding mode, with the para-chlorophenyl ring predicted to bind in the minor pocket in place of the benzimidazole (Fig. ). Many of these disparities may be explained as a result of the cumulative, per-atom application of the guidance force. Since the guidance force is added equally to all heavy atoms, it follows that placing more atoms into the guidance density will lead to a greater overall reward in the docking. This can result in inaccurate dockings for compounds like fentanyl and SR17018 where the guidance density is well defined only for a subset of ligand atoms but not all of them, inducing more ligand atoms (often from larger chemical groups) to occupy those densities, at the expenses of the smaller chemical groups which should be placed there (Fig. ). Using degraded resolution guidance density in this system had mixed effects, but once again the 4 Å density appears to display the best balance between performance improvement and detriment (Fig. ). The re-docking success rate with 4 Å maps remains 3/6 (50%). For cross-docking, meanwhile, the best success rates are seen with either the 3 Å or 4 Å resolution maps (15/30, 50%). The DAMGO peptide can be considered the most challenging ligand of this set, and required 54 hours to be docked with GlideEM 3 . In our simulations, it was docked in under 30 seconds with RMSDs below 2 Å in half of the tested receptors when using the 4 Å resolution degraded maps with consensus density guidance.