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O(N) SCGB solvation models: first “blood”

Not only our recently introduced surface charges generalized Born (SCGB) models prove to be reasonable in terms of providing solutions to Poisson Boltzmann equation in complicated geometries, such as biomolecules. By getting rid of the standard O(N^2) expression for the solvation energy we are able to formulate SCGB models in terms of a fast O(N\ln N) algorithm using FFT. The comparison between the Born radii calculated with the help of the fast method and the standard approach is presented below:




The calculation was performed for 2ht7 H1N1 neuromidase protein. The radii match over a broad range of the atoms locations within the protein. The fast method involves an (large) computational overhead due to FFT calculation and breaks even with the usual approach for any molecule exceeding about a thousand atoms.

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This entry was posted on Friday, November 27th, 2009 at 5:41 pm and is filed under Generalized Born, solvation energy. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.

One Response to “O(N) SCGB solvation models: first “blood””

  1. Quantum Pharmaceuticals » Blog Archive » O(N) Surface Charges Generalized Born calculation demonstration Says:
    December 23rd, 2009 at 7:07 pm

    [...] we reported calculation of the Born radii. Now we can use SCGB model expressions for the surface charges density to obtain the solvation [...]

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