 | | Computational
Simulation of Receptor-Ligand Energetics - For those cases where the structural
model is of high quality, molecular mechanics computational simulation techniques
will be applied to them, including full solvation, to investigate the specific
details of molecular interactions. These include minimization, Replica Exchange
Monte Carlo, and molecular dynamics, which is where most effort will be focused
as it provides the most complete picture of molecular interactions. Enhanced sampling
techniques will also be used for molecular dynamics, such as Tsallis statistics
or equal-tempering methods. These methods use non-Boltzmann sampling distributions
to provide a wider sampling of phase space than the same length standard simulation
which leads to improved average properties. These averages are computed using
techniques which recover the standard Boltzmann distribution so are directly comparable
to the experimental system. |
|
