- jfactor-1.5.3.tar.gz includes a
calculator for Jacobson-Stockmayer factor (j-factor) for a worm-like
chain with arbitrary shape and elasticity. The Jacobson-Stockmayer
factor is effective concentration (probability density) of one
terminus of a polymer chain in the vicinity of the other. The effective
concentration is computed using very efficient biased Metropolis Monte
Carlo simulations. Please cite our paper
if you use this software and remember that it is licensed under GPL v2.
- CRANKITE includes Metropolis Monte Carlo
sampler of polypeptide backbone conformations. This animation illustrates the sampler. The detailed algorithm description
is published. Inquiries regarding this
software are welcome. This software will be available in Fall 2007.
- Hydrogen bond mapping and assignment of protein secondary structure
will be available shortly. This program is based on the ideas from
DSSP, but uses customizable
hydrogen bonding criteria in geometric rather than energetic form.