Lecture GK-8

Comparative modelling

Aims

• To explain the steps involved in comparative protein modelling.
• To describe how 3D transformations are used in some modelling steps.

Objectives

After this lecture you will:

• know the steps involved in comparative protein modelling;
• understand how fragment-fitting is used in the modelling process;
• understand how structures and structural fragments can be clustered;
• understand how to compose 3D transformations;
• understand how to use 3D transformations to model protein fragments.

Supplementary Material

The lecture handout, featuring some of the lecture slides, is available on-line. (PDF)

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.

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

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

ModBase is a database of three-dimensional protein models produced by comparative modelling.

A short discussion of 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. (PubMed)