120 A Practical Guide to Cancer Systems Biology
Figure 4. Modeling with I-tasser Web. (a) Job submission form of I-tasser. (b) Result
page (partial) of I-tasser. You may download the result dataset, packed into a compressed
file, with the link provided in the top of the report (not shown).
Procedure
I. Navigate to I-tasser (http://zhanglab.ccmb.med.umich.edu/
I-TASSER/), or search it in the search engine (Fig. 4(a)).
II. Paste the protein sequence into the large input box, or upload the
sequence file by using the file upload field below. Fill the other fields
if found necessary. Entering you e-mail is recommended (Fig. 4(a)).
You may also view the options below to adjust them if needed. In most
cases, the defaults are good to go.
You may request an account and password for tracking your job progress.
III. Click ‘Run I-tasser’ below. Depending on properties of your protein, it
may take at most three to four days to finish the work.
IV. After the modeling is finished, you may navigate the result page and view
information about template, scoring, function prediction, and ligand
prediction information in this page (Fig. 4(b)).
To download everything, please use the link directly below title of the
result page.
- Homology modeling with ModWeb
You may use ModWeb (Fig. 5), which uses Modeler as its modeling engine.
Using ModWeb requires a MODELLER license key, which can be obtained
freely for academic users in http://salilab.org/modeller/registration.html.