I wanted to know whether we can observe the synergistic/antagonistic/additive properties of combinations or mixtures of compounds through docking analysis. But during docking preparation any non-standard residues will be cleaved out and I'm not able to dock two ligands in an active pocket....
The newest version of Autodock Vina should allow multiple ligand docking.
you can dock multiple ligands by scripting Perl/Python on the single receptor.
Hi Ricardo J Ferreira ... it's Alessandro, you meant simultaneous docking?
Hi Alessandro Barbieri ,
yes, simultaneous docking (I tried it). There is also another software named MLSD (multiple-ligand simultaneous docking) that is based on Autodock4 - unfortunately this one is more difficult to obtain.
You can check it here:
Multiple ligands docking — Autodock Vina 1.2.0 documentation (autodock-vina.readthedocs.io) (works quite similar to MLSD)
Ricardo J Ferreira nice, thanks, somebody suggested me this also:
https://autodock-vina.readthedocs.io/en/latest/docking_multiple_ligands.html
Hello Ricardo J Ferreira,
thank you for your kind suggestion. So this procedure in Auto dock Vina is not about screening of multiple ligands for best scoring ligand, rather analysis of simultaneous docking of two or more ligands in a protein to study their interaction with each other, with the protein and observe their biding energy scores, correct?
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