BIOL 6312
HOMEWORK
due 31 March 2003

1. Identify a protein whose structure is unknown. Select one with a sequence of 100-200 amino acids. If it is too similar to a protein of known structure, then start over with a new sequence. If you desire, you can try the first 200 amino acids of a longer protein that is of special interest to you. No membrane proteins!

2. Use BLAST to identify its closest neighbor. Submit it at the NCBI web site using the protein-protein Blast.

3. Perform two predictions of secondary structure One of the methods should be Predict Protein.

4. Perform two predictions of tertiary structure. Try Swiss-Model first (although their site is in transit to Basel, it seems to be working.) Your output here should be a pdb file.

5. Bring your pdb files to class on March 24 and we make a Chime page for viewing. (E-mail to yourself @smu.edu)

6. Your final submission on March 31 should include:

Print outs:
The name, source, and amino acid sequence of the protein.
The BLAST output of the alignment with the most similar sequence (i.e. just a few lines)
The two secondary structure predictions, about one page each.

Email:
The two pdb files. (email to me)
The html (Chime) page (I will send you a template before 24 March). (email to me)