BIOL 6312
HOMEWORK 7
due Friday, 27 April 2018

You will need the amino acid sequence of a protein with unknown 3D structure. It should not be larger than 300 amino acids, but you may try a larger protein if you wish.

To find a sequence, go to NCBI under the Protein tab and search. Select FASTA to get the sequence, which you can usually copy and paste into a web service.

Submit the sequence to at least one site for secondary structure prediction:

PredictProtein
Jpred4
PsiPred

and to at least two sites for teriary structure prediction:

Swiss Model
PsiPred (check GenTHREADER and/or pdomTHREADER)
Phyre2
I-TASSER
ROBETTA

or use the Protein Modeling Site, or links at the Protein Structure Prediction Center

Some sites may require registration, which is usually an email address. The results usually are returned within 24 hours.

The Protein Modeling Site allows the simultaneous submission to several sites for a tertiary structure prediction. Times to receive a response may vary. You should receive a pdb file, in which case you can examine the predicted structure using Jmol.

Send me a short, < 1 page, report in which you try to interpret the results, in terms of the fold, or possible fold. Does the model look like an actual protein? If you get a predicted pdb file, send the pdb file to me also.

NOTE: The predictions that are sent to you will possibly go to your Junk mail folder, so look there, if necessary.