スケール変換したエントロピーサンプリング法によるペプチド分子の構造予測

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  • Prediction of peptide conformation using a scale-transformed entropic sampling algorithm
  • スケール ヘンカン シタ エントロピーサンプリング ホウ ニヨル ペプチド ブンシ ノ コウゾウ ヨソク

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A scale-transformed entropy sampling algorithm for searching a conformational energy space of polypeptides is presented. This algorithm is based on the assumption that high energy barriers can be overcome by a uniform sampling of the logarithmically transformed energy space. This algorithm is tested with Met-enkephalin, a peptide with a known global minimum structure. Using a new Monte Carlo sampling method, energy barriers of 3000 kcal/mol are frequently overcome and, therefore, many minima are searched more efficiently than with the usual entropy sampling simulations. This method can be utilized as the optimization algorithm. The global minimum conformations obtained in optimizations agree well with those obtained by the simulated annealing (SA) method and by the sys­tematic stepsize variation (SSV) method. The entropy, the average energy and the specific heat are es­timated with one Monte Carlo run.

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