Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility.

@article{Nilmeier2008MultiscaleMC,
  title={Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility.},
  author={Jerome Nilmeier and Matt Jacobson},
  journal={Journal of chemical theory and computation},
  year={2008},
  volume={4 5},
  pages={835-846}
}
We present a Monte Carlo sidechain sampling procedure and apply it to assessing the flexibility of protein binding pockets. We implemented a multiple "time step" Monte Carlo algorithm to optimize sidechain sampling with a surface generalized Born implicit solvent model. In this approach, certain forces (those due to long-range electrostatics and the implicit solvent model) are updated infrequently, in "outer steps", while short-range forces (covalent, local nonbonded interactions) are updated… CONTINUE READING