Lecture: Structural Bioinformatics 3

Aims

• To explain the steps involved in comparative protein modelling.
• To introduce the concepts of fold recognition and secondary structure prediction.

Objectives

After this lecture you will:

• understand the objectives of comparative modelling, fold recognition and secondary structure prediction;
• know the steps involved in comparative protein modelling;
• understand how fragment-fitting and rotamers are used in the modelling process;
• be aware of the concepts of fold recognition and secondary structure prediction, and the situations where these methods could be applied.

Supplementary Material

The lecture handout contains some of the lecture slides.

A short discussion of state-of-the-art techniques in protein structure prediction, and their applications, is given in: Baker, D., and Sali, A. (2001) Protein structure prediction and structural genomics. Science, 294, 93-96. (David Baker's publication list)

Rob Russell has written A Guide to Structure Prediction that includes practical advice and links to useful software.

Several of the figures shown in the lecture were taken from Professional gambling. This is an updated version of the article: R.Rodriguez, R. and Vriend, G. (1997) "Professional gambling", in Vergoten, G. and Theophanides, T. (eds.) Proceedings of the NATO Advanced Study Institute on Biomolecular Structure and Dynamics: Recent Experimental and Theoretical Advances.

Principles of Protein Structure, Comparative Protein Modelling and Visualisation has material from an internet course on protein structure and modelling.