Future Developments
This sections lists ideas for future developments to CYCLIZE. Please let me know what you think.
  • Metropolis Monte Carlo: adds a "weighting" function during the generation of chains, increasing the number of bent chains. The summation of the distribution functions would be fractional, to make up for this weighting. The use of the Metropolis MC vs traditional MC should be a user defined parameter.
  • Adhere to the Cambridge Accord (Dickerson, et al., 1989) in terms of defining the positive roll and tilt values, and define the center of a bend to be between two base pairs, rather than at the base pair.

  • Jon Lapham
    Yale University
    Department of Chemistry - Crothers Lab