Dear rdkit Users, I made some modifications to the ligand with rdkit and I want to optimize the ligand in the protein pocket. When we performe such optimization ,we can keep all the protein atoms fixed. Or we can optimize several protein sidechains and the ligand together. Is it possible to make such optimization with MMFFoptimizer or UFFoptimizer directly?
If we can only optimize the ligand, can I add some virtual point to mimic the protein pocket environment so that the ligand wouldn't overlap with protein atoms after minimization? Many Thanks. Best, Changge Changge Ji
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