Article ID: 35 - Last Modified: May 4, 2011
Can you comment on the usefulness of running only the alignment part within CombiGlide core hopping and then using the dressed library for docking within Glide?
You can do this, but the intent of core hopping is to reproduce the pose of the original side chains while replacing the original core. Glide SP might find a very different pose. Depending on your project and intentions, this might or might not be what you are looking to do.
However, if you are confident that you are starting with a good pose of the original ligand (for instance, from a high-quality x-ray structure) and you want to retain the original side-chain interactions with the receptor, then the "normal" stage 2 refinement of the CombiGlide core hopping workflow will do this for you.
Keywords: Core hopping, Dressed library, Glide SP
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