Lecture 11

De novo protein modelling

Aims

• To introduce the ab initio protein folding problem.
• To give an overview of the protein structure prediction method of Simons et al. (1997).
• To give an overview of the zipping and assembly method.

Objectives

After this lecture you will be able to:

• describe the ab initio protein folding problem;
• describe in outline the protein structure prediction algorithm of Simons et al. (1997);
• describe in outline the zipping and assembly method.

Supplementary Material

Some of the lecture slides are available on-line (PDF).

The ab initio protein structure prediction algorithm introduced in this lecture is described in:

• Simons, K.T., Kooperberg, C., Huang, E. and Baker, D. (1997) Assembly of Protein Tertiary Structures from Fragments with Similar Local Sequences using Simulated Annealing and Bayesian Scoring Functions. J. Mol. Biol., 268, 209-225 (doi:10.1006/jmbi.1997.0959)

The zipping and assembly method is described in:

• Dill, K.A., Lucas, A., Hockenmaier, J., Huang, L., Chiang, D. and Joshi, A.K. (2007) Computational linguistics: A new tool for exploring biopolymer structures and statistical mechanics. Polymer, 48, 4289-4300 (doi:10.1016/j.polymer.2007.05.018)
• Hockenmaier, J., Joshi, A.K. and Dill, K.A. (2007) Routes are trees: The parsing perspective on protein folding. Proteins: Structure, Function, and Bioinformatics, 66, 1-15 (doi:10.1002/prot.21195)