A Monte Carlo algorithm is used to simulate the early steps of protein folding on a (2,1,0) lattice. An amino acid is randomly selected and displaced to a new available position on the lattice. The energy of both initial and final conformations is computed from the Miyazawa and Jernigan potential of mean force and the Metropolis criterion is then applied. The starting point is the protein structure in a random coil conformation and the simulation is typically of 106 Monte Carlo steps. Output data may be smoothed using a method based on Pascal's Triangle and analysis of hydrophobic residues.
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Protein intrachain contact prediction with most interacting residues (MIR). R Acuņa, Z Lacroix, N Papandreou, and J Chomilier. Bio-Algorithms and Med-Systems 10 (4), 227-242.