Bioinformatics Tools Training Program

A small molecule interacting with a protein can be modified in order to change its affinity and, in
fine, its biological activity to obtain new molecular probes or drugs. In addition, by docking the
same compound into several protein targets, one can gain insights into the underlying molecular
mechanisms of selectivity. The properties of the predicted complex can also be investigated by
further calculations, so that complex recognition mechanisms might be unveiled.

SwissDock web server
A large interest for docking web servers has emerged recently, as can be seen through the growing
list of similar web services currently available, such as DockingServer, DockingAtUTMB,
Pardock , PatchDock, MetaDock, PPDock, and MEDocK.

SwissDock is a docking web server in which the structure of the target protein, as well as that of the
ligand, can be automatically prepared for docking. In addition, the cumbersome syntax of the
docking engine is hidden behind a clean web interface providing reasonable alternative sets of parameters as well as sample input files. All calculations are performed on the server side, so that
docking runs do not require any computational power from the user.

Docking parameters
Three docking parameter presets can be selected: very fast, fast and accurate. They correspond to
presets described previously (20). In brief, several docking parameters are adjusted in order to reach
the desired docking time and exhaustiveness of the search: the number of sampled BMs, the number
of minimization steps that are performed to relax the ligand and the number of predicted BMs. If the
ligand has less than 15 rotatable bonds and/or is likely to fit exactly into a binding pocket of the
target protein, the very fast and fast modes are most probably sufficient.

Flow Chart
Target Selection – Ligand Selection – Job name – Email Address – Submit