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  • Title: Monte Carlo sampling algorithm for searching a scale-transformed energy space of polypeptides.
    Author: Nakamura H.
    Journal: J Comput Chem; 2002 Mar; 23(4):511-6. PubMed ID: 11908088.
    Abstract:
    A Monte Carlo sampling algorithm for searching a scale-transformed conformational energy space of polypeptides is presented. This algorithm is based on the assumption that energy barriers can be overcome by a uniform sampling of the logarithmically transformed energy space. This algorithm is tested with Met-enkephalin. For comparison, the entropy sampling Monte Carlo (ESMC) simulation is performed. First, the global minimum is easily found by the optimization of a scale-transformed energy space. With a new Monte Carlo sampling, energy barriers of 3000 kcal/mol are frequently overcome, and low-energy conformations are sampled more efficiently than with ESMC simulations. Several thermodynamic quantities are calculated with good accuracy.
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