This document outlines steps for docking a ligand into a protein receptor using MOE software, including preparing the protein structure, checking for necessary water or ligand interactions, validating the docking with an old ligand, and docking a new ligand if validation is successful. It also provides instructions for selecting molecules, printing results to a PDF, and identifies some amino acid types and structures.

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