2022 DOCK tutorial 2 with PDBID 4ZUD

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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

4ZUD System

Directory Preparation

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

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
4zud pdb.png

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!)