124 A Practical Guide to Cancer Systems Biology
Figure 7. Sequence identity information (marked by black box) can be obtained from
the result models of (a) SwissModel and (b) ModWeb.
Procedure
I. Navigate to ModEval page by entering its url into your browser’s nav-
igation bar (http://modbase.compbio.ucsf.edu/evaluation/) or search
‘ModEval’ in your search engine (Fig. 8(a)).
II. Fill the form accordingly, then hit ‘Start evaluating’ button (Fig. 8(a)).
III. View the result carefully. If you have questions about entries on the
page, you may click on the question mark in a blue box after each entry
(Fig. 8(b)).
Note: The lower the DOPE score is, the better the model.
Note: Please remember to save result web page for future reference.- Viewing and rendering the protein model with PyMol
After modeling is finished, you will get a pretty figure of your protein model.
However, if you wish to see it in another angle, zoom to the important sites.
Here we introduce PyMol,^16 which is capable of displaying and rendering
your protein model as you wish.
Materials
- The model(s) created by any of the protein modeling software.