Hi Khan,

Try the following WEB servers:

http://www.swisstargetprediction.ch/

http://mips.helmholtz-muenchen.de/hitpick/cgi-bin/index.cgi?content=help.html

http://prediction.charite.de/

http://sea.bkslab.org/

http://www.dddc.ac.cn/tarfisdock/

http://idtarget.rcas.sinica.edu.tw/index.php

You could also try Chemspider - it includes an algorithm called LASSO, which predicts what your molecule of interest might bind to based on similar drugs with known targets.

you'd better try a reverse docking approach where you try to find out what are the possible targets for your ligand.

Tarfish dock is quite good but you may also try

http://chemyang.ccnu.edu.cn/targetfishing/index.php to also perform MD simulations.