"Transport: A Graphical Viewer for Transmembrane Proteins"

Supervised by A.Simons

Abstract

The completion of the Human Genome Project has produced a large amount of DNA sequences that encode membrane proteins. Presently it is possible to predict which segments of the protein sit in membranes and which are outside by using simple algorithms. However the output of these systems is in a textual form, telling the user which stretches of amino acids or DNA lie in the membrane. Whilst this is useful, it is helpful and often necessary for publication, to have a visual image of the structure of the protein in the membrane. At present this image is often drawn by the researchers themselves, this can be very time consuming and can result in many different styles and systems of representing similar proteins.

Initial attempts to automate this process have been made, despite the resultant production of two working systems VHMPT and TOPO, the vast majority of academics (both computer literate and not) still produce their images themselves. The reason for this apparent anomaly is thought to be the difficulty of use of the systems and problems in the style of image produced.

The aim of this project was to automate the process of visualisation of membrane proteins. To achieve this goal a similar system to VHMPT and TOPO was developed improving attributes such as ease and simplicity of use. The system is available on the web as an applet and as an application for the user to download.