Sixth exercise: Structure prediction

Assignment due next Monday, April 23, 2007. Submit the sequence of a protein to 2 prediction servers. You may use the one from last week. First try SWISS Model. If it works, then try one more. If it doesn't give you a model, then try 2 others including Robetta. If you get a pdb file as output, make a Jmol page. Send me a short, < 1 page, report, and the Jmol page and pdb file (if the pdb was available).Use the template.html file.

1. SWISS Model

You will receive an acknowledgement from them with a password to your "workspace". You may not need it if you get the results while your page is still open.

If the modelling is successful, you will receive an email with a link to the pdb file. If no suitable homology model exists, you will receive nothing! (Like this)

With better luck (>30% sequence identity to a known structure) this. Now you have a pdb file.

2. GenTHREADER

Results for nuoC

Results by email

3. Rosetta (HMMSTR)

This will return a pdb file by email (see email) (see Jmol)

4. Robetta

You must register for this prediction service.

Here is my result for secondary structure prediction.

It claims this molecule as the template for the 3D-structure (Jmol)

For 3-D prediction, select Fragment Libraries. You will get lots of small pdb files that predict the 3D sructure of segments of ~10 amino acids.

5. Prospector

Try it

6. 3D-PSSM

New version called PHYRE

7. Fugue

Here is my result. It also gives a structure prediction in pieces.

PART 2

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