Polarized continuum solvent model: considerable acceleration with the multicharge matrix approximationстатья

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Дата последнего поиска статьи во внешних источниках: 9 июня 2016 г.

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[1] Polarized continuum solvent model: considerable acceleration with the multicharge matrix approximation / V. B. Sulimov, A. Y. Mikhalev, I. V. Oferkin et al. // International Journal of Applied Engineering Research. — 2015. — Vol. 10, no. 24. — P. 44815–44830. Molecule-solvent electrostatic interaction is considered in the frame of the polarized continuum model (PCM). The new approximate algorithm of the PCM-equation solving is suggested and it is hundreds of times faster than the exact PCM-equation solving algorithm implemented in the program DISOLV. This new algorithm is based on the novel multicharge approximation of the large dense matrix describing solvent-excluded surface (SES) discrete elements pair interactions. The algorithm is implemented in the MCBHSOLV program. The programs DISOLV and MCBHSOLV were compared for 20 proteins, ligands and their complexes. We calculated acceleration and loss of accuracy in the MCBHSOLV program for different discretization steps. We estimated discretization uncertainty, that is energy variability with the triangulation network shifting on SES. We have demonstrated, that 0.2 Å discretization step is enough to calculate the desolvation energy by the MCBHSOLV program within several minutes with accuracy of the desolvation energy calculation better than 1 kcal/mol.

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