How to dock ligand into active site with the existence of HEME?

[aw10279]

Hello, I would like to use DiffDock to generate docking conformations of a ligand in the active site of a P450 enzyme, but there's also a HEME in the active site. The docking region should be above the HEME. I tried including or excluding the HEME in the enzyme's PDB file, but found the results were similar—clearly, the model didn't account for the presence of HEME, as many conformations overlapped with the HEME. How can I achieve this type of docking prediction? Should I treat the HEME as a second ligand for prediction? However, the README doesn't provide examples of docking two molecules simultaneously. Thank you! @gcorso

[wjq1981]

I share the same confusion.