MOE - DockingTutorial
MOE - DockingTutorial
Docking Tutorial
This tutorial provides a worked example of docking in MOE. The PDE4B
receptor from the structure of PDE4B in complex with rolipram (PDB code
1RO6) will be used as the receptor for docking. Initially, we will dock rolipram
back into the receptor (self-docking) and then, in a second docking run, various
known PDE4B inhibitors will be docked into the PDE4B receptor. For the
second run, we will create a pharmacophore query prior to docking and we
will use it as a filter for docking placement.
MOE Tutorials
Conventions Used in this Tutorial
Extracted from the MOE manual In this tutorial, we will assume that you are using a three-button mouse. For
information on using a two-button mouse see Using the Mouse.
Add hydrogens and partial charges to the system with the Protonate3D
application.
The calculation will take a few moments. Progress reports are written
to the MOE window. The messages disappear when the calculation is
done. Now draw a Gaussian Contact surface around the binding site.
2
The docking results will appear in a DBV window (dock.mdb). See in
the S field that the docking poses are ranked by the MM/GBVI binding
free energy calculation which is identical to the E_refine score. Also Use the arrows of the Database Browser to browse through some of
note the rmsd field, which is the RMSD of the docking pose compared the poses returned by MOE Dock. Next, we will dock a database of
to the co-crystal ligand position. Use the Database browser to ligands to this receptor and we will filter the poses with a
compare the docking poses to the ligand in the co-crystallized pharmacophore query. Close the Database Browser and close the
structure. docking database (dock.mdb) when finished.