122 A Practical Guide to Cancer Systems Biology
It’s highly recommended that you fill in your e-mail address into the
form, since it may take a long time to finish your model.
III. Press ‘Calculate Model’. Take note of the link in the result page for
future reference.
IV. After the model is finished, you may navigate to the result page
(Fig. 5(b)).
V. Navigate to the detail page as show in Figs. 5(b–d) and inspect the
result carefully.
Note: please save the web page containing detailed description of
your mode along with your model coordinate file (i.e., pdb file)- Quality assessment with QMean server (Fig. 6)
Although the modeling report given by I-tasser, ModWeb and SwissModel
contains quality assessment, you might want to gain more confidence of your
model by submitting the model for 3rdparty inspection.
QMean score is already used in the evaluation step of SwissModel.
Materials
- The model created by I-tasser or ModWeb. (Since models from SwissModel
uses the same scoring matrix as QMean server, submitting them would be
unnecessary)
Procedure
I. Navigate to QMean server page by entering its url into your browser’s
navigation bar (http://swissmodel.expasy.org/qmean/cgi/index.cgi) or
search ‘QMean server’ in your search engine (Fig. 6(a)).
II. Fill the form accordingly. Hit ‘Submit’ to start the job (Fig. 6(a)).
III. After the model evaluation is finished, you may navigate to evaluation
report (Fig. 6(b)).
You can see global score and local score detail from the result page.
To get more information about Q-MEAN score and Q-MEAN Z-score,
please press the question mark buttons, or click on ‘help’ button in
the navigation bar under the title ‘QMEAN Server for Model Quality
Estimation’.