Embedded Files
Why Clean Protein?
When you download a protein structure (e.g., from the Protein Data Bank - PDB), it usually contains extra molecules that are not needed for docking or simulation, such as:
Water molecules (HOH).
Bound ligands or crystallization agents.
Ions and cofactors are not relevant to your study.
Alternate chains you may not want.
Cleaning ensures the protein is ready for computational experiments, like molecular docking or molecular dynamics simulations.
Protein Preparation (Cleaning)
Once installed, you can use Chimera for protein cleaning:
Opening the Protein File (Load the protein)
Launch UCSF Chimera.
Go to File → Open.
Select your protein file (.pdb) (Figure 1).
Figure 1: Chimera is launched.
2. Load the 3K35 protein (Figure 2).
Figure 2: Uploading 3K35 to Chimera
3. Click on open to view the protein (Figure 3).
Figure 3: Click to open 3K35
4. The protein structure will be displayed like the figure below (Figure 4).
Figure 3: Structure of 3K35
5. To know the number of chains that are present in the protein, click on Select → Chain. There are six chains in the structure, from chain A to F (Figure 4).
Figure 4: Structure of 3K35 showing chain A to F.
6. To select a chain of your interest, click on Select → Chain. For this tutorial, we selected chain B (Figure 5).
Figure 5: Structure of 3K35 with selected chain B.
7. To delete your chain of interest, click on Actions → Atoms/Bonds → delete. (Figure 7).
Figure 7: Structure of 3K35 with the selected chain to be deleted.
8. For this tutorial, Chain B to F is deleted, and Chain A is shown below (Figure 8)
Figure 8: Structure of 3K35 (Chain A).
9. To check the standard amino acids and the nonstandard atoms that are present, click on Select → Residue. You will find the residues in the figure below (Figure 9).
Figure 9: Structure of 3K35 (Chain A), with the standard and nonstandard residues.
10. For Molecular docking, we don't need all the nonstandard residues, so we need to get rid of them by clicking on the residue you want to delete and then clicking on Actions → Atoms/Bonds → delete. For this tutorial, we are getting rid of all the nonstandard (APR, HOH, SO4, UNX, and ZN) residues that are present in the structure. Or you can click on all nonstandards, then click on Actions → Atoms/Bonds → delete. This will delete all the nonstandards residues once (Figure 10).
Figure 10: Structure of 3K35 (Chain A) when the nonstandard residues were removed.
11. Add hydrogen
To add hydrogen, click on the following. Tools → Structure Editing → AddH (Figure 11).
Figure 11: Structure of 3K35 (Chain A) with hydrogens added
Add charges (useful for docking prep)
To add charges, click on the following. Tools → Structure Editing → Add Charge.
12. Energy minimization (optional refinement)
To minimize the Structure, click on the following: Tools → Structure Editing → Minimize Structure (Figure 12).
Figure 12: Energy minimization process for 3K35 (Cahin A)
13. Save cleaned protein
To save the PDB file, go to File → Save PDB.
Dock Prep, which is under the Structure Editing panel, is also used in protein preparation. For those who are interested in it, we will talk about it in the future tutorial.
Now your protein is ready for molecular docking.
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