I already tried SwissDock, which returned about 30 docking scenarios of the ligand bound to the protein surface. While this is interesting, I am more interested in docking the ligand in the active site to get an idea of its binding. I have heard about AutoDock, and Rosetta, but are there other, free, easy to use programs readily available for this task that have a user friendly interface?
Use Autodcok is a free protein-ligand docking software. It is available in GUI as well. It is the best software for protein-ligand docking based on Genetic algorithm. Follow these steps to proceed: http://autodock.scripps.edu/faqs-help/tutorial.
If you know the active-site information from experimental studies is fine.. otherwise predict the active site information using Ligsite/CastP tool.
Happy Docking.
In case your ligand is a peptide, there is also the CABS-dock server (http://biocomp.chem.uw.edu.pl/CABSdock/).
The ligand of interest is Farnesyl Pyrophosphate (FPP), but that is still a cool link. Thanks for the response!
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