Docking computation procedure
Known ligand (e.g. Vemurafenib or Ibuprofen)When a known ligand is selected for docking, the procedure simply consists in showing – on a new page – a 3D presentation of the pre-calculated results by the AutoDock Vina software.
New ligandWhen you are ready to predict the binding mode of the ligand you have designed, docking computation is launched on a remote computer thanks to the Internet (tens of thousands of different geometries and positions of the ligand in the protein are evaluated by using AutoDock Vina!). A page showing the procedure's progress is displayed. If all the docking processors are being used, the length of the waiting list is indicated (i.e. the number of procedures expected before yours takes place). Once it's free, computation per se begins and a progress bar is displayed.
The procedure typically lasts less than a minute - all depending on the size of the ligand and the protein's active site. When completed, the message "Docking completed! The results are shown here" is displayed. All you have to do is click on the link to see the results.