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Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
Author(s) -
Labute Paul
Publication year - 2009
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22234
Subject(s) - tautomer , macromolecule , solvation , chemistry , conformational isomerism , van der waals force , computational chemistry , ionization , hydrogen atom , chemical physics , molecule , ion , stereochemistry , group (periodic table) , biochemistry , organic chemistry
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. Proteins 2009. © 2008 Wiley‐Liss, Inc.