Estimating binding energy should be a direct outcome of molecular mechanics and computer simulation in an ideal world.  We examined the potential to reliably estimate relative binding enthalpies of a tetrapeptide to SH2, a small protein domain of ~100 residues.  In order to average over multiple simulations for computational efficiency and estimating errors, trajectories were initiated with different coordinates as well as different velocities.  Alternative local regions of a superbasin sampled by the multiple trajectories were characterized from energy-rmsd histograms and component energy variations.   The consequence for reliably estimated binding enthalpies will be discussed.

Relative binding energies by the direct method

251st National Meeting (2016)

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