Abstract
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.
Highlights
As of October 2007, The protein data bank[1] contained in excess of 45,000 structures, mostly the result of X-ray diffraction at resolution values greater than 1.5 A
One would find a definitive collection of 3D macromolecular structures containing hydrogen atoms and attempt a reconstruction of the hydrogen positions and ionization states using only the heavy atoms
We have presented Protonate3D, a method for the automated prediction of hydrogen coordinates given the 3D coordinates of a macromolecular structure
Summary
As of October 2007, The protein data bank[1] contained in excess of 45,000 structures, mostly the result of X-ray diffraction at resolution values greater than 1.5 A. E is the dielectric constant of the interior of a solute, esol is the dielectric constant of the solvent, {gi} are (topological) atom-type-dependent constants that account for nonpolar energies including cavitation and dispersion using an inverse sixth-power integral instead of surface area, {Ri} are (topological) atom-type-dependent solvation radii, j is the Debye ionic screening parameter that depends on salt concentration, {qi} are the atomic partial charges, {Bi} are the Born self-energies (inversely proportional to the Born radii), which are estimated with a pairwise sphere approximation[23] to the solute cavity, and rij denotes the distance between atoms i and j Were it not for the {Bi}, the GB/VI equations would be a pairwise potential; because the Bi of a particular atom i depends on the state assignment of atoms in other chemical groups with possibly unknown state, we must calculate a set of {Bi} that (a) remain fixed despite the protonation state of other groups and (b) reasonably preserve the GB/VI energy values. The approximation to the volume integral in the GB/VI is a pairwise summation of the form
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