Editing ChargeCalculator:Motivation (section)

=Critical elements enabling the transition between two states=

The absolute values of atomic charges cannot be validated experimentally. Sometimes these values correlate with observable phenomena (potentials, chemical shifts, etc.). However, even when the absolute values of atomic charges do not correlate with any phenomenon observable for a certain molecular system under given conditions available to the user (or in literature), it is still possible that the relative differences in charges hold further information about chemical reactivity and biological significance.

Given two states of a molecular system, patterns in charge differences can provide insight into the mechanism by which the system evolves between these states. The two states can be different conformations, mutants, ligand bound and ligand free states, etc. Look for significant differences in the charge on atoms, residues or other relevant molecular fragments. These sites are most likely important elements of the transition, and acting upon these sites can modulate the ability of the molecular system to move between the two states. Such information can be important in protein engineering, understanding disease, etc.