The Bioinformatics of Protein Structure

NB. This course is only open to those people continuing the MSc in Bioinformatics.

Course provider:	The University of Leeds
Course contact:	Brian P. Clark (bmbbpc@bmb.leeds.ac.uk)
Summary:	The aim of this module is to acquire a knowledge of the basic mechanisms of protein evolution and to use this to inform and guide the process of relating protein structure, function and primary sequence data.
Syllabus:	The course is divided into nine sections: Amino Acids and Molecular Interactions Protein Secondary Structure Domains, Folds and Motifs Introduction to Protein Evolution Classification of Protein Structure Protein Sequence Alignment Construction of Phylogenetic Trees Prediction of Secondary Structure Introduction to Comparative Modelling
Further details:	The assessment elements: for each section of the course there will be one tutorial exercise which must be completed satisfactorily; there will be three written assessments. Assessment weightings Your final grading for the module will be a weighted mean of the marks for your written assessments. Assessment 1. Protein Evolution, 20% Assessment 2. Construction of Phylogenetic Trees, 30% Assessment 3. Comparative Modelling, 50%
Technical requirements:	This module is delivered entirely via the internet, so a reliable internet commection is essential. You will need access to a PC running a recent version of Microsoft Windows (preferably Windows XP or Windows 2000), with a screen resolution of 1024 x 768. During the course you will be required to download and install programs and plug-ins which only run under Windows, so no other operating system will be supported. No browser other than Microsoft Internet Explorer is currently recommended for this module. In addition to Microsoft Internet Explorer, you will need to download and install the following plug-ins: Adobe SVG Viewer. MDL Chemscape Chime Sun Java plug-in which supports Java 1.4.
References:	1 Bioinformatics Instant Notes D.R. Westhead, J.H. Parish & R.M. Twyman BIOS; ISBN 1859962726 2 Bioinformatics: Genes, Proteins & Computers, Edited by C.A. Orengo, D.T. Jones & J.M. Thornton, BIOS (2003) ISBN 1 85996 054 5 3 Fundamentals of Molecular Evolution, (2nd Edition) Dan Graur & Wen-Hsiung Li, Sinauer Associates (2000); ISBN 0 87893 266 6 4 Biological Sequence Analysis Edited by R. Durbin, S. Eddy, A. Krogh & G. Mitchison, Cambridge University Press (1998); ISBN: 0521629713

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