User:Pakpoom Subsoontorn/Notebook/general reading/2008/10/29

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Kemp elimination catalysts by computational enzyme design

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outline

  • Computational Design
    • Choose catalytic mechanism, create idealized active-site
      • carboxyl group of aspatate or glutamate
      • imidazole, position and polarized by carboxyl group of aspatate or glutamate (His-Asp dyad)
    • H-donor group to stabilize phenolic oxygen (Lys, Arg, Ser, Tyr, His, water or none)
    • π-Stacking interaction for charge delocalization (Phe, Tyr, Trp)
  • RosettaMatch hashing algorithms