I have synthesized some small molecule. I searched in PubChem, there is no similar structure found in Pubchem database. How to identify the potential drug target for the newly synthesized small molecule. I want to know its biological activity.
Please Use TarFishDock Server(http://www.dddc.ac.cn/tarfisdock/). Here you will be able to identify the potential drug targets those can be the receptor molecule for your small ligand. Besides, you can also know whether your designed molecule can be a potential drug for any disease or not.
U can also use Pharmmapper server (http://59.78.96.61/pharmmapper/) it applies pharmacophore alignment method.
Thank you very much Roshan Meshram, Its working, Previously i was using TarFishDock, but from last few month it is not accepting any compounds (May be server of database problem). But your suggestion works for me...Thank you!!
Hi sharma, I too tried what Roshan Meshram said. But can you please let me know how to get our molecules in Tripos mol2 or MDL sdf file formate.,.
Hi, you can draw your structure in Corina 3d and save your structure in Mol format. and then you can convert it into .sdf or .mol2 format using OpenBabel software. Browse your molecule in PharmMaper and submit.
But i have used other approach. I draw the structure using Corina 3d (http://www.molecular-networks.com/online_demos/corina_demo_interactive) and save the structure in mol format. Opened in PyMOL and saved as .pdb and submitted to idTarget (http://idtarget.nchc.org.tw/idtarget/).
You can also use PRODRG server and draw your structure there and save it in MOL or Mol2 format
You can also try SciFinder or STITCH (interaction networks of chemicals and proteins), it might give you a better idea based on the similar molecules and its drug target
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