Aims

• To introduce alternative definintions of molecular surface.
• To describe alternative ways of representing molecular surfaces.
• To introduce the protein docking problem, and the Hex protein docking program.
• To introduce the structure of class II MHC molecules.

Objectives

After this lecture you will:

• understand how a probe sphere is used in defining the molecular surface and identifying surface atoms;
• be aware of polyhedral and spherical harmonic shape representations;
• understand, in principle, how surface skins can be used in predicting protein docking conformations;
• be aware of how bioinformatics techniques can be used in predicting MHC-peptide interactions.

Supplementary Material

A brief description of the molecular surface mesh program is given in an appendix of my PhD thesis (PDF, 23k).

This appendix includes some references to papers on molecular surface representation by Michael Connolly. In addition to these, Connolly has written an online 2D demo (Java) of molecular surface calculations and an interesting review article.

For information on spherical harmonic surface representation and protein docking, see Dave Ritchie's web pages. From there you can download Postscript versions of the papers on "Fast Computation, Rotation, and Comparison of Low Resolution Spherical Harmonic Molecular Surfaces" and "Protein Docking Using Spherical Polar Fourier Correlations". The docking study involving the antibody Fab - haemagglutinin complex was presented on a poster at a Structural Genomics conference in 2000 (see abstract by Hamilton, Ritchie and Kemp).

For more information on modelling class II MHC molecules, see:

Swain, M.T., Brooks, A.J. and Kemp, G.J.L. (2001) An automated approach to modelling class II MHC alleles and predicting peptide binding. Proceedings of the Second IEEE International Symposium on Bio-Informatics and Biomedical Engineering, IEEE Computer Society Press, pp 81-88. (PDF, 328k)