Wikipedia:Reference desk/Archives/Science/2019 December 30

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December 30

Is there a docking service like patchdock that will allow me to ignore "empirical" ligands crystallized in a PDB structure?

So all the PDB structures for the receptor I want (estrogen receptor alpha) are already complexed with a ligand. I get that this was necessary for crystallization, but I need to be able to remove these ligands before docking. This is ruining the comparison I want (because I would like to compare two different ligands, one endogeneous and one synthetic.) Currently the endogeneous ligand in the PDB seems to be excluding the synthetic ligand (added through a second PDB id) from the active site and this is frustrating me. Is there a way to dock "over" those ligands? Yanping Nora Soong (talk) 21:24, 30 December 2019 (UTC)