Computational methods in bioinformatics (2016-2017)

Lecture 8

Protein design; Surface Representation

Aims

Objectives

After this lecture you will be able to:

Supplementary Material

Some of the lecture slides are available on-line (1 per page, 4 per page).

The computational approach used to design Top7 is described in:

Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L. and Baker, D. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science, 302, 1364-1368 (doi:10.1126/science.1089427 )

Some creative ways of combining antibody domains to form novel engineered proteins are shown on Nico Mertens' web site.

The solvent accessible surface was proposed in: Lee, B. and Richards, F.M. (1971) The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol., 55, 379-400 (doi:10.1016/0022-2836( 71)90324-X).

A brief description of the molecular polyhedral shape representation program is given in an appendix of my PhD thesis (PDF).

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.


Last Modified: 27 November 2016 by Graham Kemp