Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal

Abstract

ABSTRACT We present performance-guaranteed approximation algorithms for the protein folding problem in the hydrophobic–hydrophilic model (Dill, 1985). 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 that 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) or quadratic time and achieve a three-dimensional protein conformation that has a guaranteed free energy no worse than three-eighths of optimal. This result answers the open problem of Ngo et al. (1994) about the possible existence of an efficient approximation algorithm with...