Proteins Structure Function and Bioinformatics · 2008 · 574 citations · 40 references
Life SciencesBiochemistryChemistryComputational ChemistryStructural BiochemistryStructural BiologyComputational Molecular BiophysicsConformational AnalysisMacromolecular Structure DeterminationProtein ConformationProtein StructureStructure PredictionComputational Molecular ModelingComputational Structure PredictionIonizationIonization StatesMolecular Conformation PredictionPredictionProtein Structure DeterminationRotamer Prediction
A new method, called Protonate3D, is presented for the automated prediction of hydrogen coordinates given the 3D coordinates of the heavy atoms of a macromolecular structure. Protonate3D considers side-chain "flip," rotamer, tautomer, and ionization states of all chemical groups, ligands, and solvent, provided suitable templates are available in a parameter file. The energy model includes van der Waals, Coulomb, solvation, rotamer, tautomer, and titration effects. The results of computational validation experiments suggest that Protonate3D can accurately predict the location of hydrogen atoms in macromolecular structures.
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