A Complete and Effective Move Set for Simplified Protein Folding

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A Complete and Effective Move Set for Simplified Protein Folding

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by Neal Lesh , Michael Mitzenmacher , Sue Whitesides

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47 - 1 self

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@MISC{Lesh_acomplete,
    author = {Neal Lesh and Michael Mitzenmacher and Sue Whitesides},
    title = {A Complete and Effective Move Set for Simplified Protein Folding},
    year = {}
}

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Abstract

We present new lowest energy configurations for several large benchmark problems for the two-dimensional hydrophobichydrophilic 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.

Keyphrases

general term pull move generic implementation novel set local search algorithm energy configuration valid configuration two-dimensional hydrophobichydrophilic model interactive optimization system rapid development subject descriptor several large benchmark problem tabu search human-guided search

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