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  • Oral presentation
  • Open Access

Assignment of protonation states and geometries to macromolecular structures using Unary Quadratic Optimization

  • 1
Chemistry Central Journal20082 (Suppl 1) :S13

  • Published:


  • Hydrogen
  • Free Energy
  • Hydrogen Atom
  • Optimization Procedure
  • Ionization State

A method is presented for assigning protonation states and hydrogen atom geometry to macromolecular structures. Tautomer and ionization state (including metal ligation) are taken into account during a large scale free energy optimization. This discrete optimization is performed with a Unary Quadratic Optimization procedure. The thermodynamic theory and the results of several computational validation experiments will be presented.

Authors’ Affiliations

Chemical Computing Group, 1010, Sherbrooke Street West, Suite 910 Montreal, QC, Canada H3A2R7


© Labute 2008