A complete and effective move set for simplified protein folding

  • Lesh N
  • Mitzenmacher M
  • Whitesides S
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Abstract

We present new lowest energy configurations for several large benchmark problems for the two-dimensional hydrophobic-hydrophilic model. We found these solutions with a generic implementation of tabu search using an apparently novel set of transformations that we call pull moves. Our experiments show that our algorithm can find these best solutions in 3 to 14 hours, on average. Pull moves appear quite effective and may also be useful for other local search algorithms for the problem. Additionally, we prove that pull moves are complete; that is, any pair of valid configurations are mutually reachable through a sequence of pull moves. Our implementation was developed with the Human-Guided Search (HuGS) middleware, which allows rapid development of interactive optimization systems.

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Authors

  • Neal Lesh

  • Michael Mitzenmacher

  • Sue Whitesides

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