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"GEM" -- Analytical Poisson-Boltzmann
Electrostatic interactions are a key factor determining
properties of biomolecules. Ability to compute electrostatic potential
generated by a molecule is often essential to understand the mechanism
behind its biological function such as catalytic activity or
ligand binding. To obtain the electrostatic potential everywhere in space,
the (linearized) Poisson-Boltzmann equation -- 2nd
order PDE -- is usually solved, traditionally by numerical approaches.
We are working on a new theory -- ALPB -- which allows one to compute
electrostatic potential around biomolecules
orders of magnitude faster (and with much less memory needed)
than the traditional approach based on numerical solution of the PB equation.
A software package GEM has been developed, mainly by John Gordon, to visualize
and manipulate electrostatic potentials. Remarkably, it was the ability to
visualize and compare approximate analytical potentials with the exact
and numerical references that allowed us (this part is mostly due to Andrew Fenley), after many a trial and error, to understand and capture
the key physics of the problem in the form of a very simple analytical formula.