hi.
I am synthetic organic chemist and working on synthesis of biologically active natural products and derivatives. I am new in the field of molecular docking. please guide me how can i select suitable protein to run the docking of my synthesized ligands. if anyone knows about helpful online tuturial/book, please share.
Thanks
Hi Aisha,
If you are interested in identifying potential receptors for a particular compound or compounds Swiss target Predictions can do so. Subsequently you need to do docking and MD simulations to validate affinity.
http://www.swisstargetprediction.ch/
Hi there...
I would recommend you to use Maestro-Schrodinger-suit. A full collection of Maestro training material is available right through training portal.
https://www.schrodinger.com/maestro
Dear Dr. Saddiqa,
Do you have any idea about the biological activities of your compounds? If so, then your target proteins are restricted to a limited number. The structure of these proteins can be downloaded from the protein data bank (https://www.rcsb.org) to be followed by a routine docking procedure with a suitable docking software. You would get better results if you also dock a known ligand that is related to your compounds to the same proteins so that you could compare the results. A good guiding tutorial for beginners (the point where I started understanding this subject) is found at (https://www.youtube.com/watch?v=rVXrbTeaywc&t=1s) by Dr. Nehru V Sankaranarayanan, thanks to her. She used two popular and free software, UCSF Chimera ( https://www.cgl.ucsf.edu/chimera) to handle the protein and AutoDock Vina (http://vina.scripps.edu) to carryout the docking process.
On the other hand, if you don't have any idea about the biological activities of your compounds, then you may try software that predict the biological activities of any compound like Way2Drug, mentioned to you by Dr. Dash, or Molinspiration Cheminformatics ( https://www.molinspiration.com), and, after prediction of the target protein , you could start the docking procedure.
Apology for the long explanation.
thankyou Dr Amily for valuable suggestions. currently i am using MOE. should i swithched to UCF or autodock? Moreover, I have checked the activity of one of my synthesized ligand from Molinspiration and the software says that it is protease inhibitor. when I searched HIV-protease from PDB, it showed a list of protease proteins. Please suggest that in this case I need to run the docking of my ligand with all mentioned proteins?
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