Homology Modeling: Protocols and Concepts 

Class Location: NCI-Library, NCI-Frederick, MD
Date: 04/17/2003
Click here to view the class notes

Exercise 2: Homology Modeling with Swiss-PdbViewer. We are going to use Swiss-PDBviewer and Swiss-Model to model the sequence of P12065. The structure for P12065 is already known (PDB:1ALC) but for this exercise we are going to pretend that we do not know the structure for this protein.

  1. Click open the Swiss-PdbViewer (Fig). Preferences >> Network Type in the File Server www.swissmodel.unibas.ch and for port 27000. Click here to see the picture. Note that the "Path of local PDB files" decides the directory where SwissPDBViewer decides to store the downloaded files.
  2. For help at any time, click the question mark looking symbol, HELP
  3. Also click on Preferences >> General... and UNCHECK "Show Log File Upon Loading" and the "Show Log file upon loading".
  4. Go to Swiss-Prot database by clicking here Enter P12065 to do a quick search. Upon entering the P12065, scroll down the end of the page and click on "P12065 in FASTA format" to download the lysozyme in fasta format. (Tip: save it under c:\temp\spdbv\download)

Threading:

  1. Load the raw sequence you have just downloaded to model
  2. Make sure the email address is given correctly at the Preferences option
  3. Ask SwissModel to find Appropriate ExPDB tempates
  4. Submit. You should see the templates (if any) in a web-page format.
  5. Choose the tempate(s) and save it in your PC
  6. Load the templates
  7. Hide the model sequence using control panel and recenter the view.
  8. Dispaly the sequence alignment and pick one template and activate it.
  9. Fit >> Magic Fit the templates. Note the Magic Fit superimposes the templates in the 3-D space and will not take into account the sequence information. Observe the sequence window for any changes. Calculate RMSD ?
  10. Try Iterative Magic Fit. Did you observe any change in the sequence alignment? Note the iterative magic fit also calculates the structural alignment automatically. Calculate RMSD ? Did RMSD value change from the previous calculation?
  11. Now choose the model sequence and make it active. Do a magic fit. Explore the sequence alignment.
  12. Go to the control panel and make the model visible.
  13. Do a Magic Fit. You should see the sequence threaded onto the template.
  14. Evaluate the structure, by displaying the secondary structure, B-factor, Secondary structure by sucession, Plot the Ramachandran plot etc.

Automatic Homology Modeling

Submit the sequence to the Swiss-Model and get the results back in a project file. Explore the built model using Swiss-PDBviewer. How does this model compare with the pdb:1ALC? Download the 1ALC using Swiss-PDBviewer, and superimpose it with the predicted 3D-model. 


Contact Info: Dr. S. Ravichandran 
              Advanced Biomedical Computing Center, 
              NCI-Frederick, 
              Bldg 430, Frederick, MD 21702
              Tel:  301-846-1991 
              Email: sravi@ncifcrf.gov