2023 DOCK tutorial 1 with PDBID 4S0V

Introduction

This tutorial will walk you through the steps necessary for using the DOCK software package. Many drugs are small molecular compounds that attach, or bind, to a protein in our bodies to change how that protein functions. By changing the function of a protein we can treat disease and help people manage symptoms of disorders. Traditionally drug discovery was done through a type of "trial and error" process called High Throughput screening. Scientists would chemically make, or buy, thousands of small compounds and expose cells to them to see which responded, either favorably or unfavorably. This method is time consuming and expensive. It would be better if the scientific community could "screen" these molecules using a computer before creating/buying compounds - thereby focusing the cost and effort on those which showed the most promise computationally. The DOCK software brings this drug discovery process into the 21st century and uses computers to bind these small molecular compounds to a protein and evaluate the results. DOCK uses algorithms to bring together the small molecule, known as the ligand, and the larger protein, and "DOCK" them together. Our tutorial will walk you through preparing a protein and ligand for DOCK'ing using an example complex from the protein data bank (https://www.rcsb.org/), complex # 4S0V.

Learning Objectives

• Understand why DOCK was created and its current role in drug design
• Gain the ability perform virtual screening of small molecular compounds to a protein from the Protein Data Base (https://www.rcsb.org/)