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On the Intractability of Protein Folding with a Finite Alphabet of Amino Acids

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Abstract.

We describe a proof of NP-hardness for a lattice protein folding model whose instances contain protein sequences defined with a fixed, finite alphabet that contains 12 amino acid types. This lattice model represents a protein's conformation as a self-avoiding path that is embedded on the three-dimensional cubic lattice. A contact potential is used to determine the energy of a sequence in a given conformation; a pair of amino acids contributes to the conformational energy only if they are adjacent on the lattice. This result overcomes a significant weakness of previous intractability results, which do not examine protein folding models that have a finite alphabet of amino acids together with physically interesting conformations.

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Received June 1, 1997; revised March 13, 1998.

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Atkins, J., Hart, W. On the Intractability of Protein Folding with a Finite Alphabet of Amino Acids . Algorithmica 25, 279–294 (1999). https://doi.org/10.1007/PL00008278

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  • DOI: https://doi.org/10.1007/PL00008278

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