This tutorial teaches you how to dock a drug molecule to a receptor.

Introduction

What is DOCK?

Many drugs are small molecular compounds that attach, or bind, or a protein in our bodies to change how that protein functions. Traditionally drug discovery was done through a type of "trial and error" process. The DOCK software brings drug discovery into the 21st century and uses software to bind thousands of small molecular compounds to a specific protein and evaluate the results. The software brings together the small molecule, known as the ligand, and the larger protein and "DOCK"s them together. This 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.

Directory layout

Example Complex PDB #4S0V

Preparation of the ligand and protein

Evaluating the Structure

Preparing the Protein file

Preparing the Ligand File

Checking Hydrogen Atoms and Atom Charges

Creating the Protein Binding Site Surface

Creating the Required Surface (DMS) File

Generating Spheres for the Binding Site

Selecting the Appropriate Spheres

Generating the Required Box and Grid

Generating the Box

Generating the Grid

Docking

Energy Minimization Steps

Footprint Analysis

Rigid Docking

Fixed Anchor Docking

Flexible Docking

Virtual Screening a Library of Available Ligands

Virtual Screeni mpi

Virtual Screening Output

Cartesian Minimization

Docked Molecules Rescoring

2023 DOCK tutorial 1 with PDBID 4S0V

Contents