Software

by Alexei Podtelezhnikov for biomolecular modeling and analysis
  • 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. I.
  • 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.