Efficient Conformational Search Method for Peptides and Proteins: Monte Carlo Minimization with an Adaptive Bias

  • Ozkan S
  • Meirovitch H
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Abstract

The energy function of a protein consists of a tremendous number of minima. Locating the global energy minimum (GEM), which corresponds to the native structure, is a severe problem in global optimization. The commonly used Monte Carlo minimization (MCM) method is based on a random selection of torsional angle values. We suggest selecting these values with biased probabilities depending on the increased structure- energy correlations as the GEM is approached during the search. Our method applied to models of the 5-residue peptide Leu-enkephalin finds the GEM ∼2.7 faster than MCM

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Authors

  • S Banu Ozkan

  • Hagai Meirovitch

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