Frequently Asked Questions
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Note that we use the provided email address only to let you know that the results are ready. However, If you prefer not to use email notifications, write down the 10-digit ticket generated for your submission and check the status of your job using the "Job Tracking" form in the right sidebar. Or don't close the confirmation page - it will refresh automatically after the results are ready.
The simulation time depends on several factors: the length of the protein, the number of identified templates and the workload on our computer cluster. Typically, the results should be ready within 1-3 days for most of the webservices.
The results will be kept on the server for one month.
Although we tested the Java applet used to visualize the results for eThread and eFindSite across several platforms, operating systems and web browsers, users may still experience some issues. If problems with Java supported features persist, please try to clean cache or use "no Java" link when clicking on "View results". We will continue working on the web interface to improve the visual components of our services.
Yes, eFindSite (1.1 and later) runs under Mac OSX. You need gcc 4.4 compiler as explained in the manual. Also, Affinity Propagation is disabled, so binding pockets are identified using an average linkage clustering algorithm.
eFindSite can predict binding pockets and binding residues. Then you can use ligand docking software, e.g. eSimDock, to dock your ligand to the predicted pocket(s).
Because of both computational requirements as well as threading issues. Threading may not work well for multiple domain proteins; a 600aa protein is very likely to have multiple domains. In that case it is much better to chop the sequence into domains and model them separately. You can try to run such targets through some servers to detect domain boundaries and then model them individually.