Before you turn this problem in, make sure everything runs as expected. First, restart the kernel (in the menubar, select Kernel$\rightarrow$Restart) and then run all cells (in the menubar, select Cell$\rightarrow$Run All).
Make sure you fill in any place that says YOUR CODE HERE
or "YOUR ANSWER HERE", as well as your name and collaborators below:
NAME = ""
COLLABORATORS = ""
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.
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.
Chapter contributors: