Task: You are to fold this protein (protein-T), given by its sequence: 

ASN LEU TYR ILE GLN TRP LEU LYS ASP GLY GLY PRO SER SER GLY ARG PRO PRO PRO SER


You assume that nothing is known about this protein, and no similar ones 
are available. This is the so-called "de-novo" folding, the essence 
of the "Protein Folding" challenge. 


Steps: 

1. Familiarize yourself with the probelm. E.g. 

http://en.wikipedia.org/wiki/Protein_folding
http://folding.stanford.edu


2. We will approach the problem in two ways. First we will try to simplify 
the original probelm -- full atomic detials in 3D -- as much as possible, and 
solve the simplified problem first. Specifically, download 
from library and skim through "Emergence of Preferred 
Structures in a Simple Model of ProteinFolding" by 
Hao Li,RobertHelling,*Chao Tang,t Ned Wingreen, Science  VOL. 273 * 1996, 
page 666. In particular, the model used in Eq. 1. 

Second, we will try to figure out what kind of numerical method we will need 
to solve the full problem. We will come up with "energy landscapes" that 
mimic real ones and see which methods work. 


Once we are done with the above, we will use a commercial code AMBER (available 
on the class machine) and the method you have identified, to actually try 
to fold the protein and visualize results using free software VMD 
http://www.ks.uiuc.edu/Research/vmd/.