In all structure-related practicals, you will use Rasmol. Before you begin, check here to find out if you have Rasmol installed and if your browser is configured properly !

To help you find the databases and servers later, there is a collection of useful links (you may want to bookmark that page).

Most of the practicals below contain a number of questions, and many of the answers are given at the end of each practical. You can record your own answers by editing a file as you go along and compare them to our answers once you have finished the practical.

Don't be afraid to ask for help or explanations !

1. Structural databases - This practical is intended to introduce you to a number of structure-related resources and tools available through the Internet.
   Level: easy
   Time: 1-3 hours

2. Structure prediction - In this practical, we will look at some structure-prediction techniques (secondary structure, helical trans-membrane regions, and fold recognition) and try to assess how reliable these methods are.
   Level: intermediate
   Time: 1-3 hours

3. Model validation - This practical will introduce you to some concepts and tools to help you evaluate the quality and reliability of protein models.
   Level: intermediate
   Time: 2-4 hours

4. 3D Motif recognition - This practical will teach you how to find occurences of small structural motifs (e.g., a set of active-site residues, or an interesting piece of main-chain structure) in the structural database.
   Level: intermediate
   Time: 1-3 hours

5. Structure recognition - This practical will introduce you to a number of web-servers that enable you to compare an "unknown" protein structure to a database of known structures. If no structural neighbours can be found, your protein may have a new fold. Otherwise, the neighbours help you classify your structure and may even provide clues that relate to the function of your protein.
   Level: advanced
   Time: 2-4 hours

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