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I'm looking to dock a large ligand (~90kDa) to a receptor slightly larger receptor (~125kDa) using Hex. If anyone is familiar with docking large structures, are there any recommended parameters for finding the best docking solution?

Parameters in particular:

  • Number of Solutions
  • N order of correlation for initial and final searches
  • Receptor Range
  • Ligand Range
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While I have no experience with this specific question you have, according to Feinstein & Brylinski (2015), a "fully automated procedure", i.e. a Perl script, can be used to optimize the box size itself, and it can be found here.

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