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