Docking via MOE 2022 -1
1 like638 views
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.
Related topics:1 of 11
More Related Content
What's hot (20)
Ad
More from mennaqansouh (10)
Ad
Recently uploaded (20)
Docking via MOE 2022 -1
- 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