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

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.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Labute, P. Assignment of protonation states and geometries to macromolecular structures using Unary Quadratic Optimization. Chemistry Central Journal 2 (Suppl 1), S13 (2008). https://doi.org/10.1186/1752-153X-2-S1-S13

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  • DOI: https://doi.org/10.1186/1752-153X-2-S1-S13

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