Protein Folding — Lattice HP Model

In the HP model (Lau & Dill 1989), amino acids are classified as Hydrophobic (red) or Polar (blue). The energy is −1 for each non-bonded H-H contact (hydrophobic core). Protein folding seeks the minimum energy conformation. Metropolis MCMC explores conformational space via pivot moves — accept if ΔE < 0, or with probability e^−ΔE/T. Finding the ground state is NP-hard in general!