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

DOI: 10.1186/1752-153X-2-S1-S13

Published: 26 March 2008

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

(1)
Chemical Computing Group

Copyright

© Labute 2008