Any folding algorithm requires…
- …a search strategy, an algorithm to generate many candidate structures (or decoys) and…
- …a scoring function to discriminate near-native structures from all the others.
In this workshop you will write your own Monte Carlo protein folding algorithm from scratch, and we will explore a couple of the tricks used by Simons et al. (1997, 1999) to speed up the folding search.
- K. T. Simons et al., “Assembly of Protein Structures from Fragments,” J. Mol. Biol.
268, 209-225 (1997).
- K. T. Simons et al., “Improved recognition of protein structures,” Proteins 34, 82-95
- Chapter 4 (Monte Carlo methods) of M. P. Allen & D. J. Tildesley, Computer
Simulation of Liquids, Oxford University Press, 1989.