search

MolecularAI / ReinventCommunity

MIT License
150 stars 56 forks source link

Constraint on key interactions while integrating DockStream with Re-INVENT #32

Closed shkao closed 2 years ago

shkao commented 2 years ago

Hi,

First of all, thank you for the great work of developing and releasing these invaluable resources! I recently integrated the docking score as a reward/score component using DockStream (AutoDock Vina). I wonder, would it be possible to set a constraint on key interactions during docking, in other words, can I provide my own pharmacophore hypothesis as a setting for filtering? Or, filtering on critical protein residues with certain interactions after analyzing using PLIP. Is there any similar functionality already?

GuoJeff commented 2 years ago

Hi @shkao,

Sorry for the delayed response. The implemented version of AutoDock Vina in DockStream does not support any docking constraints (I believe a newer version of AutoDock Vina does). By contrast, Glide supports constrained docking and you can enforce hydrogen bond interactions to be retained. The result is REINVENT learns to propose compounds which satisfy your desired docking constraint. Using Glide however requires a Schrodinger license as it is a proprietary software.

shkao commented 2 years ago

I see, thank you, @GuoJeff !