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Assignment of Protonation States and Geometries to Macromolecular Structures using Unary Quadratic Optimization
Paul Labute, CCG
Many computational methodologies relating to macromolecular structures depend significantly on the assigment of protonation states and proton coordinates. The complexity of hydrogen bond networks, tautomers, ionization states and metal ligands often make automated protonation assignment quite difficult. A method based upon Unary Quadratic Optiimization is presented to address this problem. The algorithm and theormodynamic theory is described along with some validation results on high resolution crystal structures.
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