This practical is intended to introduce a number of tools available throught the internet for dealing with aspects of protein structure and function. We will use the structure of the bacterial enzyme subtilisin, examine its structure with regard to function, and how it relates to other proteins with similar function.

Practical by Tom Taylor and adapted by Gerard Kleywegt. © 1998-2002.

How this practical works

Most of the tools required for this practical are available over the net. Since it will be most convenient to use two browser windows, one to read the instructions and one to perform the database searches etc., all hyperlinks will open into a new browser window (don't forget to close the ones you won't be needing anymore).

In most places you should attempt to find the information you require yourself. Where appropriate, you will find a red ball near the instructions which you can click on if you get stuck. This is your cheat button. Click on the cheat button to the right -->

When you have worked through a set of instructions, clicking the "Next" button at the bottom of the page will take you to the next page. You can go backwards by clicking on the "Previous" button. You can also use the pop-up menu below to go to a specific page directly.

As you go throught the practical, make notes on what results you find, how you got there and any thoughts you have on the method. These may come in useful for you later when you need to make database searches or use web-based tools in other situations.

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

Before you begin with this practical, make sure to ask your tutor how to set up your browser to deal with the display of protein structures (e.g., using Rasmol). You can use this page to check if you have Rasmol installed and if your browser is configured appropriately.

If you are not familiar with protein structures at all, you may want to read chapter 5 of "Introduction to Bioinformatics" by A.M. Lesk. A more thorough introduction can be found in chapter 1 ("The Building Blocks") of the book "Introduction to Protein Structure" by Brändén and Tooze (and possibly chapters 2-6 as well). Alternatively, you can have a look at this brief introduction on the web, or at this more extensive one.

The review paper "Catalytic triads and their relatives" (G. Dodson and A. Wlodawer, Trends in Biochemical Sciences (TiBS), Vol. 23, September 1998, pp. 347-352; PubMed) provides some background information about serine proteases and their active sites.


If you have previously started with this tutorial and wish to continue, select the section with which you want to continue from the pop-up menu below and then hit the "Go !" button.

Good luck and have fun !



Practical "Structural Databases" - EMBO Bioinformatics Course - Uppsala 1999/2001 - Gerard Kleywegt

Latest update at 6 February, 2002.