2022 DOCK tutorial 2 with PDBID 4ZUD
DOCK is a molecular modeling program capable of sampling lower-energy ligand conformations with respect to a binding surface on a given protein. DOCK utilizes and manipulates the geometry of the ligand to find the conformation that yields that most favorable interaction with the respective binding site. With this tool, millions of molecules can be rapidly screened against a target protein for the purposes of identifying new drug molecules that are physiologically relevant.
For more information on DOCK and it's uses, please refer to their online manual: DOCK6 Manual
Before beginning, create the following directories in your space so that all necessary files are organized and can be access quickly:
mkdir 001.structures 002.sphere_selection 003.gridbox 004.dock
You don't have to name your directories the same as they are named here, but be cautious since the files that will be used for this tutorial utilize this naming scheme. They will need to be changed in each file that refers to them if you don't use this naming scheme!
Be sure to have Chimera installed on your system as it will be our primary visualization and system-editing program.
Protein and Ligand Preparation
Download the 4ZUD PDB file from the RCSB PDB website and open the file in Chimera.
Select -> Open -> (pathway to pdb file on your local machine) -> Open
You will notice a few side chain residues are explicitly displayed; those are the ones that directly engage with the ligand. The structure also has some missing regions denoted by the dashed-lines. These regions do not have to be modeled to use the system for docking since the majority of the protein remains restrained during the process (except for the residues of the active site, to a certain extent). You can play around with Chimera and visualize the protein from different angles to get a complete look at the protein to ensure there are no glaring errors in the structure that could have somehow arose from the downloading and opening process (Doesn't usually happen, but it's always good to be sure before moving on!)
Many structures deposited in the PDB lack hydrogens due to the difficulty in resolving their electron densities from cryo-EM or X-ray crystallography. The structures also lack formal charges since that information is not captured with out current experimental structure-determining techniques. Both charges and hydrogens are crucial for accurately studying any chemical system, and so they both must be added manually to 4ZUD in order to prime the system for docking.
We first want to select everything but the ligand (we will deal with the ligand in the next step). A straight forward way to only select the protein is to first select the ligand:
Select -> Residue -> OLM
And then press Shift + Right-Arrow keys on your keyboard at the same time to invert the selection to everything but the ligand (which in this case is just the protein!)
To add the hydrogens to the protein:
Tools -> Structure Editing -> AddH
All residues in the protein should now have all of the hydrogens that were missing. Make sure to look at the output log of this command just in-case any errors arise, although there should be none if the instructions were followed thus far.
There is a similar Chimera command to add charges to your protein selection:
Tools -> Structure Editing -> Add Charge
After using this command you should receive an error stating that Correct charges are unknown for 3 non-standard atom names in otherwise standard residues. If you look at those atoms in the reply log, they're hydrogens belonging to ILE53. If you take a look at the paper that accompanies the 4ZUD structure, those hydrogens were replaced by tritium for crystallization purposes and Chimera does not recognize them as standard atoms and doesn't have predefined partial charges for them. Since Chimera doesn't recognize them, it will not apply charges to them. Additionally, since they are just hydrogens (meaning that their charge contributions to the system is often times very minimal) and the residue is not near the ligand active site, we do not have to do anything further in terms of adding charges.
The Add Charge command predicts the ligand net charge to be -1. This makes sense since the ligand has a deprotonated carboxylic acid group. It's always good practice to look at the ligand structure and make sure that the predicted charge makes sense. It's also important to look for the ligand charge in the corresponding paper to make sure everything is consistent!
4ZUD Structure Caveat In the 4ZUD paper it mentions that ILE53 was mutated to an Alanine, but when you load the PDB into Chimera, it is recognized as an isoleucine but with an alanine side-chain.
There is no immediately obvious explanation for this, but since it is being recognized as an isoleucine, we're just going to edit the side chain to be the correct one. ILE53 can be selected by using the following command on the Chimera Command Line interface which could be accessed under Tools: