Polypeptide Structure
We are developing Monte-Carlo methods to sample the configurational space
of polypeptide molecules in-vacuo in order to learn about
the relative contributions of different functional groups and interactions
to structure. We have developed and utilized sophisticated sampling
methods which combine simulated annealing and parallel tempering
algorithms and allow one to overcome large energic or entropic barriers
which lead to quasi-ergodic sampling. One of the strengths of the new
techniques is their parallel nature which enables the time-consuming
calculations to be carried out on our beowulf cluster,
racaille.
These methods are currently being utilized to estimate lifetimes and
rate constants for conformational changes. This is being carried
out using transition state pathways and geometrical order parameters.
Pictures
Structure
of 10 Residues of Glycine (100.3 K)
Structure
of 5 Residues of Lysine (62.4 K)
Created by Jeremy Schofield
Last modified: Thu Feb 24 17:53:20 EST 2000