hello all. I want to make a comparative study between a docking with and without water molecules.
I have used CCG MOE, but not for docking. For docking, I use Autodock or Autodock VINA, using YASARA as a graphical front-end.
In general, for docking you must remove ligands and water from the receptor to prepare it for docking with a ligand. However, if you have information indicating that one or perhaps more specific water molecules is/are involved in the binding of a ligand to a receptor, then you could make these waters part of the receptor before docking.
Information on waters that might be participating in ligand binding include consistently finding specific water molecules that form hydrogen bonds with the ligand and receptor in several crystal structures. Descriptions of these critical interactions with specific waters would most likely be included in the papers associated with the crystal structures.
Dear Farid,
To make the most of our software, different option are available for you, to get a specific answer according to your needs, please contact us using this email adress: [email protected]
I am wondering how one can retain only the waters in the active site through using MOE software
- Badges
- Science topic
- Similar topics
- Microbiology
- Assays