82 research outputs found
Absolute FKBP binding affinities obtained via non-equilibrium unbinding simulations
We compute absolute binding affinities for two ligands bound to the FKBP
protein using non-equilibrium unbinding simulations. The methodology is
straight-forward, requiring little or no modification to many modern molecular
simulation packages. The approach makes use of a physical pathway, eliminating
the need for complicated alchemical decoupling schemes. Results of this study
are promising. For the ligands studied here the binding affinities are
typically estimated within less than 4.0 kJ/mol of the target values; and the
target values are within less than 1.0 kJ/mol of experiment. These results
suggest that non-equilibrium simulation could provide a simple and robust means
to estimate protein-ligand binding affinities.Comment: 9 pages, 3 figures (no necessary color). Changes made to methodology
and results between revision
Resolution exchange simulation
We extend replica exchange simulation in two ways, and apply our approaches
to biomolecules. The first generalization permits exchange simulation between
models of differing resolution -- i.e., between detailed and coarse-grained
models. Such ``resolution exchange'' can be applied to molecular systems or
spin systems. The second extension is to ``pseudo-exchange'' simulations, which
require little CPU usage for most levels of the exchange ladder and also
substantially reduces the need for overlap between levels. Pseudo exchanges can
be used in either replica or resolution exchange simulations. We perform
efficient, converged simulations of a 50-atom peptide to illustrate the new
approaches.Comment: revised manuscript: 4.2 pages, 3 figure
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