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.

Objectives

After this lecture you will:

• understand how a probe sphere is used in defining the solvent accessible surface and the molecular surface;
• be aware of spherical harmonic surfaces;
• understand, in principle, how surface skins can be used in predicting protein docking conformations.

Supplementary Material

A brief description of the molecular surface mesh program is given in an appendix of my PhD thesis (PDF). The surface mesh construction described in that appendix is referred to as an alpha shape in:

Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V. and Subramaniam S. (1998) Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins, 33, 1-17 (PubMed)

Liang, J., Edelsbrunner, H., Fu, P., Sudhakar, P.V. and Subramaniam S. (1998) Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins, 33, 18-29 (PubMed)

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 PDF versions of the papers about this work and slides from Dave Ritchie's presentations.