Three servers have been developed for this purpose:
PharmMapper Server is a freely accessed web-server designed to identify potential target candidates for the given probe small molecules (drugs, natural products, or other newly discovered compounds with binding targets unidentified) using pharmacophore mapping approach. Benefited from the highly efficient and robust mapping method, PharmMapper bears high throughput ability and can identify the potential target candidates from the database within a few hours.
ReverseScreen3D is a reverse virtual screening tool that searches against a biologically-relevant and automatically-updated subset of ligands extracted from the RCSB Protein Data Bank in order to identify potential target proteins that are likely to bind a given compound.
Similarity ensemble approach (SEA)
The Similarity ensemble approach relates proteins based on the set-wise chemical similarity among their ligands. It can be used to rapidly search large compound databases and to build cross-target similarity maps.
Read also the relevant paper:
"Target fishing and docking studies of the novel derivatives of aryl-aminopyridines with potential anticancer activity."
Bioorg Med Chem. 2012 Sep 1;20(17):5220-8. doi: 10.1016/j.bmc.2012.06.051. Epub 2012 Jul 11.Erić S, Ke S, Barata T, Solmajer T, Antić Stanković J, Juranić Z, Savić V, Zloh M.
Thanks to Mire Zloh for this information!
If you have more servers in mind, please let us know!