Abstract

) William E. Hart y Sorin Istrail z Dedicated to Professor Solomon Marcus on the occasion of his 70th birthday Abstract We present performance-guaranteed approximation algorithms for the protein folding problem in the hydrophobichydrophilic model, Dill (1985). To our knowledge, our algorithms are the first approximation algorithms in the literature with guaranteed performance for this model, Dill (1994). The hydrophobic-hydrophilic model abstracts the dominant force of protein folding: the hydrophobic interaction. The protein is modeled as a chain of amino acids of length n which are of two types: H (hydrophobic, i.e., nonpolar) and P (hydrophilic, i.e., polar). Although this model is a simplification of more complex protein folding models, the protein folding structure prediction problem is notoriously difficult for this model. Our algorithms have linear (3n) time and achieve a three-dimensional protein conformation that has a guaranteed free energy within 3=8 of optimal. By ac...

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