I have seen some research papers on molecular docking studies using some conformer-generating softwares like CORINA, OMEGA, etc. and they used these softwares to generate conformers of a molecule and they used these conformers for the later docking. Is this really necessary? The docking programs will calculate and remodel the conformers again later though. I was thinking, perhaps, if we dock these conformers but the docking programs have to only fit (evaluate), not doing any change to the structure of the molecule. Can AutoDock or any other software be limited to perform this step only?
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3 Answers
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No, you don't need to generate a library of conformers before docking.
I personally advise again that, except if you have a chemical/biological justification to use your own library.
One of the strength that a package has is the method it uses to search for the complex best pose.
Software like GOLD used genetic algorithm to generate its library whereas GLIDE make use of systematic search, for example.
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Autodock vina is a docking software that doesn't need to manually add every conformers of the ligand because they will be generated on the basis of rotable bonds of the ligand.
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From my perspective, if you are new to this field, I agree with Camps. Softwares like Glide or GOLD already have builtin process which are more easy to follow than building your own libraries for docking.
If you are interested in speeding up your conformational searching process, and generating some more initial conformers with higher quality, as mentioned in Benchmarking Commercial Conformer Ensemble Generators, other softwares such as Omega, which focused on conformer generation can have better performance.
