Small molecule ligand dynamics during refinement

Hello there,

I am docking a small molecule ligand into a protein and wanted to ask if the ligand is able to explore different conformations during refinement. For example, could a substituted cyclohexane ring sample different chair/twist-boat conformations? Alternatively, is rotation of a substituted phenyl substituent attached to the rest of the molecule via a rotatable single bond possible?

Best wishes,


Hi Justin

In principle yes. But it depends on the topology generated by PRODRG.
You can also provide an ensemble of conformation for your ligand, sampling those with another software prior to docking.

I would however not expert the boat/chair conformations to be sampled during refinement.