Aims

• To reinforce the use of a probe sphere in defining the molecular surface.
• To give practice in using macromolecular docking software.

Objectives

After this practical you will:

• have used a program that demonstrates the principles of molecular surface calculations;
• have used the Hex macromolecular docking program;
• will be able to initiate a docking calculation using Hex, and view the predicted docked conformations.

Introduction

In this tutorial you you will use the Hex macromolecular docking program. If you need help using this program during the tutorial, please ask. If you need help when working on your own, a useful starting point is the Hex User Manual.

To run Hex, type:

    hex

Exercises

1. Experiment with Michael Connolly's 2D demo (Java) of molecular surface calculations.

2. Use Hex to perform a local docking search with the antibody HyHel-5 and its antigen, lysozyme. Do this by following the steps at the start of section 5 and in section 5.5 of the Hex User Manual. As docking proceeds, look at the output in the "Hex Messages" window. When docking is complete, step through the top predictions interactively, and compare these visually with the native docked conformation.