Homology Modeling Using SwissMod

SwissMod website allows users to carry out model building for proteins of unknown structure by employing homology to proteins of known structure.

Copy the sequence in the problem to the clipboard, and take the link above to SwissMod. You will be presented with this page:

Select the Automated Mode from the menu at the left (the top item). This page will appear:

Fill in your email address and a title for the project. Then paste the sequence into the large box, and click the button at the bottom. (Ignaore the advanced options.)

The first part of the results will look like this:

You may wait for the results to be displayed - anywhere from 10 minutes to 10 hours, depending on how busy the server is. Alternatively, close your browser. An email will be sent to you when the project is done, with a link to the results.

If you have waited, this screen will ultimately appear:

Alternatively take the direct link in the email sent to you, which lead to this same web page.

Clicking on the graphic of the structure brings up a window similar to a Jmol window.

You can right click on the Download as PDB link below the picture, and choose Save As to save a PDB file of your predicted structure. At the right of the page is a link to download the whole page as a PDF file.

This page last modified 2:28 PM on Thursday March 3rd, 2011.
Webmaster, Department of Chemistry, University of Maine, Orono, ME 04469