Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.

@article{Brgi2002SimulatingPA,
  title={Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.},
  author={Roland B{\"u}rgi and Peter A. Kollman and Wilfred F van Gunsteren},
  journal={Proteins},
  year={2002},
  volume={47 4},
  pages={
          469-80
        }
}
For the structure and function of proteins, the pH of the solution is one of the determining parameters. Current molecular dynamics (MD) simulations account for the solution pH only in a limited way by keeping each titratable site in a chosen protonation state. We present an algorithm that generates trajectories at a Boltzmann distributed ensemble of protonation states by a combination of MD and Monte Carlo (MC) simulation. The algorithm is useful for pH-dependent structural studies and to… CONTINUE READING
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