Covalent docking of Inhibitors to crystal

[Hariharan-Annadurai-bit]

hello, I am curious whether this approach of covalent docking can be extended to non-protein structures like heme and other small molecules.

[diogomart]

It can, yes. Do you have more details about your system?

[Hariharan-Annadurai-bit]

So I am trying to dock one of the molecules of this dimer(https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=AYILIE&DatabaseToSearch=Published) onto the other guided via covalent docking. In short, I am splitting the dimer into monomers and see how they interact. When I did the conventional docking, the rings' pi-pi stack on each other which may not be the actual crystal structure so I am trying to see if the covalent or reactive docking works in this regard.

[diogomart]

I think conventional docking is more appropriate for this system. You may want to try the AD4 scoring function with +2 charge on the irons.