Alpha-Helix Folding: Hydrogen-Bond Cooperativity

This simulator runs a coarse-grained Metropolis Monte-Carlo model of alpha-helix formation directly on a peptide backbone. Every residue carries a coil/helix flag; four consecutive helical residues close one backbone hydrogen bond between residue i's carbonyl and residue i+4's amide, and the whole configuration's free energy follows a Zimm–Bragg-style nucleation-plus-propagation model, so helices form the way real proteins do — a costly nucleation event followed by cheap, cooperative growth. Raise the temperature to melt the helix back to random coil, switch to a glycine-rich or proline-kinked sequence to see how amino-acid identity controls helix propensity, and watch the live helix-content, hydrogen-bond count and radius of gyration track the folding in real time.