Fifth exercise: Predict Protein
1. Download the new template/jmol files sit zip
Included is a templete for a 2-molecule page, and one for an Introduction/Table of Contents
When you make a tutorial with multiple pages, you should link each page:
Next Previous Introduction or Table of Contents
2. Now let's look at the pages submitted: 6312 links page
Think about sizes, colors and placement of text.
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
3. Type in the name of a protein or gene and Click "Go". (If you have no ideas try nuoF)
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
14. Examine sample output: For Web viewing, For Printing
15. Assignment: Submit a sequence for secondary structure prediction and write a short report about the results
16. This will be due on Monday, April 18.
Comments/questions: email me
Copyright 2005, Steven B. Vik, Southern Methodist University