2021 DOCK tutorial 1 with PDBID 1HW9

DOCK

DOCK 6 is one of the many tools available to computational biologists that predicts ligand binding geometries and interactions. The functions of DOCK 6 are diverse and have several general applications. A primary use of the program involves a virtual screening of thousands of molecules for an intended purpose. These purposes can include database screenings for molecules that inhibit enzyme activity, bind a particular protein, or even bind to larger complexes. As more versions of the program are released, new features are added such as the inclusion of solvation and receptor flexibility considerations in its calculations.

IHW9

IHW9 is the PDB code for the catalytic complex between human HMG-CoA reductase (HMGR) and Simvastatin. HMGR is considered a rate-controlling enzyme in the metabolic pathway responsible for the biosynthesis of cholesterol. Inhibitors of HMGR, known as statins, are often prescribed as treatment therapies for high cholesterol patients. While statins inhibit the catalytic effect of HMGR, they also provide other positive biochemical effects such as the stimulation of bone growth and anti-inflammatory responses. Studying statin binding using this complex can potentially aid in the discovery of drugs capable of producing these off-target effects.

Directory Preparation

Before even beginning the DOCK prep, it's much easier to create the directories we'll be using throughout the calculation now rather than later. To begin, make a directory using the PDB code provided on the website. This makes organizing the files cleaner and easier to follow.

  mkdir 1HW9

Once the directory is made, enter it as we will be creating several more directories within this directory.

  cd 1HW9

Inside the 1HW9 directory, you should make several additional directories with the following titles. You do not have to follow the same nomenclature provided here as these are simply examples. However, the names you ultimately choose should be indicative of the information you will be keeping in them. This makes finding files much easier later on in the DOCK process.

  001_structure  002_surface_spheres  003_gridbox  004_dock  005_virtual_screen  006_virtual_screen_mpi  007_cartesianmin  008_rescore

You can confirm the presence of these directories within 1HW9 by using the "ls" command.