THE GALLERY - Examples

Example Course Material

Page currently under construction!


Students are warned that they may struggle on the course without some knowledge of the fundamental disciplines involved. Prerequisites are listed in Some teaching material on these prerequisites is available through the course pages. As an example, see some geometry prerequisites provided by Stefan Sack.

Here is a quick Introduction to the Amino Acids

From the Course Backbone

Introductory material includes an introduction to the basic structure and geomety of proteins. The two most important elements of protein "secondary structure" are covered in detail. Oliver Smart at Birkbeck has produced an excellent overview of molecular forces . WARNING! - this section is complex, mathematical, and long!

A comprehensive section on protein secondary structure by Kurt D. Berndt includes to a link to an email server for the program PredictProtein . This predicts the secondary structure of a protein based on its sequence similarity to other proteins of known structure. Its use is free to academics and students.

The overall structure of proteins, divided into classes, is covered in detail. Examples include:-

These pages contain links to many examples of protein structures, taken from the Protein Data Bank at Brookhaven, USA.

Proteins are classified into "folds" using a system based on their overall topology. There are very many fewer known folds than known structures. Folds are further classified into structural classes - an example is all-beta proteins.

Links are available to two databases of protein structure classification:

The final part of the course examines ways in which proteins interact with each other and with other large molecules in cells.

Protein Families

Material describing a number of protein families in detail is planned. Some of the first example families are:-


Cytokines are "extracellular messengers"; when they bind to receptors embedded in the cell membrane, signals are transmitted into the cell.

Author: Simon Brocklehurst.

Zinc Metallo-Proteases

Proteases break down other proteins by selectively cleaving peptide bonds. There are several families of proteases. The metalloproteases bind a metal ion - often zinc - in the active site. Carboxypeptidase A and thermolysin are well-known examples.

Author: Daniel Barsky


The small hormone, insulin, was one of the first proteins to be crystallised and solved. It can associate into dimers (two molecules) and hexamers (6 molecules).

Insulin is not, strictly speaking, a "protein family"; this section, with impressive inline graphics, is included here in recognition of the part played by Dorothy Hodgkin in the development of protein crystallography.

Authors: Raj Gill and J. Walshaw, University of London.


Molecular Movies

AVI Movies
These molecular animations, contributed by Andrew Booth of the BioNet Teaching & Learning Technology Project, are in the form of .avi files. You will need a viewer such as Media Player to view them. They are large files, between 0.5 Mb and 8 Mb.

Example subjects are the transition between oxy-and deoxy-haemoglobin, and the transmembrane helices of rhodopsin with a chromophore bound.

A movie from Joel Sussman, Richard Gilliland, and Daniel Ripoll, showing how substrate moves into the active site of acetylcholinesterase.

MIME tutorial

Henry Brzeski of Strathclyde University has written a tutorial to illustrate the use of the molecular graphics program RasMol to study the lac repressor / operator complex and its interaction with DNA. [To run the tutorial, you need a Web browser configured to start up RasMol automatically when a Protein Data Bank file is imported.]

Lectures and Conferences in BioMOO

Neuroscience Journal Club
Transcript of a recent discussion of a paper in Experimental Neurology held at BioMOO, with participants from 3 continents. An archive of journal club transcripts can be found here .

Guest Lecture
A lecture and question and answer session on sequence analysis given by Dr. William Pearson as part of the GNA Virtual School of Natural Sciences course on Bioinformatics (June '95).

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