Step 0
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Click "Service" in the menu.
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Click "Service" in the menu.
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Specify the query protein that you are interested in. You may
specify the query protein either by providing a PDB ID or by
uploading a file in PDB format. "substructure of interest" is an
optional field. If "substructure of interest" is left blank, then
the entire protein will be examined. An example for this field is
as follows:
*:A, *3:A, *4,5:A, *6-9:A, *LEU:A,
where *3:A stands for the third residue in chain A and *LEU:A
stands for all LEU residues in chain A.
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In this page, you can adjust several settings to make the search
results fit your expection. Due to the automatic extraction
mechanism, Protemot contains more than 2000 templates and is
still increasing along with PDB. The number in brackets is the
database size. Please choose the most specific template library as
possible. Another way to increase the performance of Protemot is
to increase the filtering level. Our experiment results show that
our filtering algorithm has very tiny effect on prediction quality.
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Please check your query again at this step, then click "submit" and
your search task will be launched. There are three ways to get the
search report. A brief report will be sent to the following e-mail
address when your serach has completed. After clicking "submit",
you will be directed to the progress page which includes up-to-time
information of your search task. The third way is to remember your
task ID and get the on-line report by the ID any time.
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This page shows up-to-time information of your search task which will
refresh every 5 seconds by default. You can change the refresh
interval as you want or check the progress of another task
(remember to click "set" after entering the new refresh interval).
Click "report" to see the final report of your search task when
the status becomes "finished".
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The report page will list the templates similar to the substructure
of the query protein which means that the query protein could have
similar functional sites to these templates. You can click the
template name to get more information about that template or click
"show" to view the alignment results in 3D. In the 3D view, yellow
portion represents the residues of the query protein which are
successfully aligned; pink portion represents the template; and
other portion represents the query protein.
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