Fifth exercise: Predict Protein

1. First take a look at the pages submitted last week

2. See: 6312 links page

Think about sizes, colors and placement of text. You should begin working on your final project now.

3. Today we will look at the Predict Protein page for submitting a secondary structure prediction

1. First you need to obtain the amino acid sequence of a protein-preferably one whose 3-D structure has not be determined.

2. Go to the NCBI site and select Protein as the database

http://www.ncbi.nlm.nih.gov/

3. Type in the name of a protein or gene and Click "Go".

4. Click on one of the file names

5. Click on the Button "GenPept" and change to FASTA

6. Click Display. Now you can see the amino acid sequence.

7. Copy the sequence after selecting it first.

8. Now go to the Predict Protein site http://www.predictprotein.org/

9. Click on "submit" a protein sequence for prediction

10. Paste your sequence in the large box.

11. Type in your email address. Use your smu.edu address to identify yourself as an academic.

12. Type in a name for the protein, to identify it to you later.

13. Click the "Submit/Run Prediction" button near the bottom. (You will get the default prediction if you do not make any other selections.)

14. Examine sample output: For Web viewing, For Printing

15. Submit your sequence to another site: http://bioinf.cs.ucl.ac.uk/psipred/

16. It may take up to 24 hours to receive your results. If you do not receive anything, you should submit another time.

17. Assignment: Analyze the results for secondary structure prediction and write a short report about the results. Consider what kind of fold your protein might be. If it is larger than 150 amino acids it might have several domains. Compare the two predictions.

16. This will be due on Monday, April 16.