2021 DOCK tutorial 1 with PDBID 1HW9
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 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.
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.