LCB EMBO UU

P.S.P.S.

Protein Structure Practicals Smörgåsbord

Here are links to the various protein-structure-related practicals in the EMBO course. You can decide yourself which of the practicals you want to do, and in which order, so you can tailor this session to your own needs and interests.

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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Latest update at 30 August, 2001.