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THE GENERALIZED BORN APPROXIMATION

Performance of the GB model relative to PB in large-scale conformational changes.

Table: The change in electrostatic part of solvation free energy, $\Delta G_\mathrm{el}(N) - \Delta G_\mathrm{el}(U) [Kcal/mol]$, of apo-myoglobin and protein-A in going from the native (N) to the unfolded (U) states calculated with PB and GB models based on Bondi radii set. Here $GB^{AO}$ is the new GB model currently implemented in AMBER-7, and $GB^{ST}$ is the ``standard" one (AMNBER-6). Each state is represented by 50 snapshots form an MD simulation.

E-mail: onufriev@scripps.edu