Docking via MOE

1. Docking via MOE
Menna AbdElshaheed

2. 1. Protein, structure preparation
2. Protonate 3D
3. Correct
4. Check ligand interactions (water) needed or not ??
5. SEQ … Check water/ Ligand
6. Saving prepared protein
Menna M. Abdelshaheed

3. Ligand inside receptor
Software 1 using the same old ligand (Validation)
Software 2 using the same old ligand (Validation)
Software 3 using the new ligand (Docking)
Rmsd < 1.5 …. valid
Rmsd >1.5 ….not valid Menna M. Abdelshaheed

4. Validation …..
Open the prepared protein (very important)
Prepared protein
1
2
3
4
5
Menna M. Abdelshaheed

6. Validation… rmsd <1.5 to be valid

7. Keep it opened (IMPORTANT)
Menna M. Abdelshaheed

8. Ligand
Ligand interactions
Ligand : Overlay complexes
Apply
Menna M. Abdelshaheed

10. 1. Select mol, S and rmsd (ctrl to add
selection)
2. File > print
3. Microsoft print to PDF
4. Use selected Fields only
5. Fit width
6. Depicted
7. Color Het atoms
8. Print > choose folder and write file
name
Menna M. Abdelshaheed

11. 1115 amino acid And type ?
Phenylalanine …. Alpha helix
1130 ??
Tyrosine … lobes