You might try pharmacophore mapping. There is a web server that does this:

http://59.78.96.61/pharmmapper/

You might try pharmacophore mapping. There is a web server that does this:

http://59.78.96.61/pharmmapper/

Dear Claudia,

You can go through these web based servers via Idtarget, Similarity Ensemble Approach, ReverseScreen3D etc. In fact I have read one beautiful article regarding the same. Please find the link http://link.springer.com/article/10.1007%2Fs12154-015-0135-3#page-1. Hope that it may fulfill your needs.

Dear Claudia,

This is a very difficult task to recognize your biological target based on your ligand. There are various ways to list the potential targets (an experimental testing is almost necessary). 

Inverse docking which involves docking a single ligand into the structures of all available structures present in the PDB corresponding to your host (say, human, Human PDB structures). Another approach is that you compare your own ligand with all the crystal ligands (co-crystallized with protein), if you get similarity, there might be a possibility to your ligand may interact with these "co-crystallized" proteins. There are also options to compare network/pathway based analysis.

You may like to see my papers on this topic: 

http://pubs.rsc.org/en/Content/ArticleLanding/2014/MB/C4MB00058G#!divAbstract

http://onlinelibrary.wiley.com/doi/10.1002/jmr.2353/abstract

Hi Caludia,

The first simplest way is Protein data Bank itself !

Protein data bank  --> Search (on your left) --> ligand search ( where u can draw or paste the molecular structure)

This gives you the possible rug targets for your molecule.

If you are an user of Scrodinger, you can use Qikprop to do the same.

Thank you !

Thank you everyone, very usefull tips!