HW. Fold a protein with your bare hands.
Purpose To give you an idea of what folded and unfolded peptide
chains and protein structure elements look like.
To make you aware of the importance and difficulty
of the problem. Not so much to give you hints towards the ab-initio, single algorithm solution you will have to find for the class project -- that one will
be different from the hands-on game of this homework.
Preliminaries. (1) Go to Fold It Scientific Game. Follow links from the front page
to learn what that is,
and why solving the protein folding problem is important for mankind.
In particular, read short article 1 and short article 2 .
(2) Download and install FoldIt code on your computer.
Create an account with FoldIt. While you are taking the class,
please do not join groups, participate in competitions,
or try to get a "global score".
Begin by completing first 12 Intro Puzzles from FoldIt. These
will demonstrate the very basics of structure manipulation tools available
in the game. Just follow their prompts. In each case what you are doing,
in effect, is minimizing energy of the system -- the score that is displayed
at the top is the ``depth" of the current energy minimum; the higher the
score the lower is the energy (the better).
Once done with levels 1-12 of the intro puzzles, click "Science Puzzles"
from the main menu, check "show expired" and "show beginner" boxes, and then
download actual Science Puzzle: "Easy Mini Freestyle". Those who
can not access this one for whatever reason, go to "Scorpion Toxin" puzzle
Use FoldIt tools that you have learned to "fold" this protein -- what
you want to do is to create a compact, hairpin-looking structure without
clashes (or at least a compact structure for the Scorpion Toxin). It should
be fairly easy to get a score of at least [7800 for "Easy Mini" or 4500 for "Scorpion Toxin"]. You can stop once this
score is achieved, or you can try to get a better score, if you wish.
You can see other people's scores in a small window.
Take a screen shot of your
highest score solution (make sure the score is shown) and submit it as a PDF file, with your last
name and homework number in the file name. The submission should be
a single page: 1/2 page discussion (in your own words) of what FoldIt is
and why protein folding is an important problem, and why it is a hard one.
The last 1/2 page is the screen shot. That's all.