BIOC0036

Protein Structure and PyMol

The aim of this practical is to ensure you have a good understanding of protein structure and that you understand the power of using protein structure to examine the effects of mutations. In particular you will:

Learn the basic use of the PyMol molecular graphics program to examine protein structure
Study phi and psi torsion angles and the Ramachandran plot
Identify structural features such as the active and binding sites of an enzyme
Map mutations onto protein structure to understand their possible effects on protein function

This web-based practical will guide you through using PyMol - a molecular graphics program - to examine protein structures. You will also look at some Bioinformatics resources to obtain protein sequence related data and mutation information.

Instructions

Throughout the practical, the aim of what you are trying to do is shown like this. Make sure you read this before proceeding, to ensure you understand the purpose behind the next steps.

Throughout the practical, important notes are shown like this.

Use the menu at the top of the page to navigate the sections of the tutorial. Work along each item in turn, or use the "Continue" button at the bottom of each page.
Read all the information on each page! It's there for a reason!!!
A useful tip is only to click links with the left mouse button. The links in the practical will all open the relevant pages in one second window. This stops you from opening dozens of windows and getting confused!
A link displayed like this will display a pop-up with more information when you click on the link.

Warning! You must record information as you go along where instructed to do so. This will enable you to answer the questions in the quiz at the end of the tutorial.

When you need to record information it will be highlighted like this.

When you complete the quiz, you will be asked to enter your name and email address to confirm that you have completed the tutorial.