The document provides instructions for docking molecules using MOE software. It describes how to:
1. Prepare molecule structures in Chemdraw and import them into MOE databases as SMILES strings.
2. Prepare protein structures by protonating and minimizing them, then remove water and other ligands.
3. Dock the prepared ligand databases into the binding site of prepared protein structures and analyze the highest scoring poses.
4. Overlay and export the best docking pose in both 3D and 2D views to analyze the ligand interactions.
4. • Draw structures in Chemdraw … transfer to moe by SMILES each one
alone (IMP)
• Prepare 1st structure then make a new database File>New> database
• At the new database add the prepared structure (edit>new>entry)
• MOE > Close (RHS) to remove 1st structure then add the second one
by smiles, prepare it...etc
• After adding all prepared molecules in the same database, Save the
database now from its window (File>save as> prepared database
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5. 1- Go to browse to save
the process … choose
your folder then write
file name
Site ..
1-Ligand atoms > Means the
same old site of the old
ligand
as in validation
or
2- Dummies > different site
Ligand ..
-The old ligand (ligand atoms)
means the ligand which was
downloaded with protein)
or
-New ligand (database) (MDB
file)
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6. With the ligand in the background, prepare it
1-Compute > Prepare >
Partial charges
2-Compute> Energy minimize (Gradient > 0.001) 1
2
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8. Notice that the prepared ligand is present in the background (IMP)
Entry = data
Field = column
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For example
9. Inside the database window itself
File, save as
Just notice the format
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After adding all
the prepared molecules in
the data base >> save it
Take care !! Don't select and don't
choose selected only
11. 3WZE
Protein > structure preparation > protonate 3D > correct >
close
Remove water (only if not involved in interaction)
Remove impurities (any ligands other than the drug)
With the prepared protein in background …. Compute >> dock
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12. Docking of the new ligands (mdb) in the site of the old ligand (site: ligand atoms)
Double click to open it
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14. Now the first pose
is the best pose
(highest score)
File > browse
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15.
16. Overlay best pose 3D:
First color the old ligand (select>ligand>atoms)
Go to Results window (sorted)….File> browse> 1st (best pose)> atoms (color)
Don’t close the window until you save the picture !! (IMP)
Save picture > format: JPG
Overlay best pose 2D:
While opened in browser (File> browse)
Ligand> ligand interactions> overlay complexes> Apply> Export> JPG, white>
browse to save
2D of best pose
Ligand> ligand interactions
• Receptor : receptor atoms
• Ligand: Browser atom
• Apply
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