This notebook contains material from PyRosetta; content is available on Github.

Introduction to Folding

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.

Suggested Readings

  1. K. T. Simons et al., “Assembly of Protein Structures from Fragments,” J. Mol. Biol. 268, 209-225 (1997).
  2. K. T. Simons et al., “Improved recognition of protein structures,” Proteins 34, 82-95 (1999).
  3. Chapter 4 (Monte Carlo methods) of M. P. Allen & D. J. Tildesley, Computer Simulation of Liquids, Oxford University Press, 1989.
In [ ]:
 

Chapter contributors:

  • Kathy Le (Johns Hopkins University); this chapter was adapted from the PyRosetta book (J. J. Gray, S. Chaudhury, S. Lyskov, J. Labonte).