I ran the entire core hopping procedure and I thought it would output the same results as running the core hopping alignment followed by HTVS in Glide using the dressed library. However, the results are different. Can you help me to understand why?

The core hopping workflow is not equivalent to HTVS. Remember that the intent of core hopping is to replace the original core while retaining the poses of the original side chains. Therefore, the docking performed in the core hopping workflow is more like a minimization in place. With this in mind, be sure to provide a reasonable starting pose in the first step of the core hopping workflow since the ligand side chains will stay in roughly the same place as they were in the original starting pose.

Keywords: Core hopping, Alignment, Dressed library, Glide docking, Minimization, CombiGlide

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