Molecular Dynamics Group, University of Queensland
Molecular Dynamics Group, University of Groningen




As it is not possible to observe individual atoms or molecules directly, various models are used to describe and/or predict the properties of a system. In this respect the personal image of an atom or molecule will strongly depend on the models with which one has been presented. The sophistication of the model we choose depends on the property in which we are interested. Normally it is advisable to choose the simplest representation that will illustrate the property of interest satisfactorily.

Examining a three-dimensional model of a molecule, one which shows the spatial relationships between atoms, is often the best way to understand the system. A physical model of a small molecule with less than 20 atoms can be easily made from plastic or wire in a few minutes. Building a similar model of a protein can take months or years. Over the last decade a combination of computer graphics and molecular modelling techniques has resulted in unprecedented power to create and manipulate three dimensional models of molecules using computers.

Nevertheless, be cautious. The images created on the screen can be very convincing. When using a program to predict a particular property of the system always be aware that the underlying model may or may not bear any relationship to reality.

About the Course

This course is designed to provide a basic introduction to the computer aided modeling of biomolecules such as proteins, nucleic acids and lipid bilayers. The exercises will concentrate on the manipulation of protein structures and assumes a basic knowledge of protein primary and secondary structure.

There are several short courses on protein structure available on the web. One developed by Georges-Louis Friedli can be found at http://­­herbs/­phytochem/­proteins.html.

Another course on protein structure (Principles of Protein Structure, Comparative Protein Modelling and Visualisationt) developed by Nicolas Guex and Manuel C. Peitsch GlaxoWellcome Experimental Research S.A. can be found at http://­­course/­course-index.htm

Some aspects of modeling techniques have been covered in the lectures. A number of web-based courses have also been developed at different institutes. Two examples which describe the theoretical principles underlying this work are:

The aim of this practical is twofold:

  1. To demonstrate the power of a modern modeling package.
  2. To examine the link between the representation style and the information content.

Getting Started
MD Theory
MD Practice

©2005/2007 T.A.Wassenaar/A.E.Mark