Volume 2 Supplement 1

3rd German Conference on Chemoinformatics: 21. CIC-Workshop

Open Access

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

  • Paul Labute1
Chemistry Central Journal20082(Suppl 1):S13


Published: 26 March 2008


HydrogenFree EnergyHydrogen AtomOptimization ProcedureIonization 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, Montreal, Canada H3A2R7


© Labute 2008