Up to now, there have been at least two schools of thoughts among those trying to calculate electrostatics part of solvation energies. Half of the folks believe that only an exact solution of the Poisson equation can be better than the solution of the Poisson equation. The other half believes that though the exact solution of the Poisson equation can be obtained, it is too slow and numerically unstable. Here in Quantum we attempt to give Generalized Born models almost infinite credit of trust and push for a direct link between the Poisson equation solutions and Generalized Born models.

The missing link between the two worlds is established by the equation linking the Born radii with the water polarization charges on a molecular interface. If the surface charges are then interpreted on their own, we can calculate the solvation energy using its direct definition, rather than an approximate Born formula. The question is of course if it all works in real life.

To proof the concept we attempted the calculation of the solvation energies for about 580 proteins from our Quantum Pharmaceuticals target list of proteins with available 3D structure. The results obtained with 4 different types of Surface Charges Generalized Born (SCGB) models are compared with the Surface Electrostatics solutions of the Poisson eqaution and are summarized below:

Here the surface electrostatics solvation energies are measured along the horizontal axis, the vertical axis is used for the SCGB solvation energies values. The green dots represent SCGB model with FSBE radii, yellow and red dots are SCGB models with respectively. All the three models give exact solvation energies for an arbitrary system of charges within a shpere and cope fairly well with the realistic proteins. SCGB with standard CFA Born radii (the blue dots) are completely off. Given tremendous speed advantage of SCGB models over SE we end up with an approximation worth to be employed!

Related posts:

1. O(N) Surface Charges Generalized Born calculation demonstration
2. FFT acceleration demonstration for (surface)GB methods
3. How to use Born surface charges to calculate solvation energy?
4. Surface GB models: the ultimate test
5. O(N) SCGB solvation models: first “blood”