Protonation states and assignments of the charges on each protein were based on standard templates as part of the Molegro Virtual Docker program, and no other charges were necessary to set.
The docking procedure involved the preparation of the ligand and macromolecule, the assignment of Gasteiger charges, and the identification of the torsional root and the two rotatable bonds of the ligand.
Because deconvolution entails the assignment of a charge state and the recalculation of the m/ z's as if the charge were +1 (decharging), the combinatorial explosion problem mentioned above is automatically eliminated.
Mismatches, due to the assignment of the same financial charge code to two or more different drugs ranged from 0.69%to0.73%3%.
In public database, 3D-conformations of the chosen chemicals were generated by omega after the removal of molecules with a hypervalent metal complex due to the assignment of charge under the Merck molecular force field (MMFF) [14, 37].
Particularly important was the assignment of positive charges in the connecting loops between the transmembrane helices to mimic the mutation experiments of Seppälä et al. (2010).
This is because under low-energy conditions, the b-ion and y-ion fragments co-exist in a loose complex; the two members of this dimer compete for the proton, with assignment of charge being determined by the proton affinities of the two ions (Paizs and Suhai, 2004).
Generally speaking, we avoid the assignment of formal charges, since this implies, in many cases, assumptions about the oxidation numbers of atoms or charge distribution within chemical moieties that are not always obvious, especially if we want to make such assumptions in a more or less automated way.
The assignment of formal charges of Cu+, S- and S 2 2 − was actually based on the interpretation from X-Ray photoelectron spectroscopy (XPS) [45].
Charge state assignment was further confirmed by theoretical simulation of the charge state distribution corresponding to the empty capsid (in absence of both VP4 and RNA) using the software SOMMS.
