- Protein Structure Modeling 119
VIII. Read the text below ‘Search for Templates’. If you accept the term
below, hit ‘Search for Templates’ to begin structure modeling.
If you do not want to participate in template searching process, press
‘Build Model’ instead and go to step X.
IX. After template searching is completed, inspect the list and choose
the best one for your situation. You may click on the ‘v’ icon in
the end of the row for some more information of the alignment.
After you select the best template, click the ‘v’ icon in the end
of the row and hit ‘Build Model’ button to make the model.
Please DO NOT close your browser if you didn’t fill your email when
submitting your modeling job.
X. When the modeling is completed, you may navigate to the result
screen, inspect the report about information of the models and
beautifully-drawn figures about the models. You may download the
parts you need, or download everything by clicking on the ‘download’
icon, which is under your project title and the right side of ‘Model’
tab (Fig. 3(c)).
Downloading everything and saving them to your disk is highly
recommended.
- Homology modeling with I-tasser web
There are some differences between I-tasser and SwissModel.
First, SwissModel will model the part with acceptable templates, thus
some part of the heading and tailing sequence of your input might not be
modeled and cannot be found in your resulting model. On the other hand,
I-tasser will strive to model the whole protein for you. In almost all cases,
everything in your input sequence will be presented in the model which is
produced by I-tasser.
Second, I-tasser will try to do function and ligand prediction for the
best model of its output. This might be helpful if known information of this
protein is too few.
Materials
- Sequence of your protein of interest. To get sequence of a protein, please
check the previous sections.