Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal
STOC '95 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing
Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
On the complexity of protein folding (abstract)
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Approximation algorithms for protein folding prediction
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
A complete and effective move set for simplified protein folding
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
The algorithmics of folding proteins on lattices
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Long proteins with unique optimal foldings in the H-P model
Computational Geometry: Theory and Applications - Special issue: The European workshop on computational geometry -- CG01
An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model
GECCO '05 Proceedings of the 7th annual conference on Genetic and evolutionary computation
Heuristics, optimizations, and parallelism for protein structure prediction in CLP(FD)
PPDP '05 Proceedings of the 7th ACM SIGPLAN international conference on Principles and practice of declarative programming
Protein folding in the HP model on grid lattices with diagonals
Discrete Applied Mathematics
Delta: a toolset for the structural analysis of biological sequences on a 3D triangular lattice
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Twin Removal in Genetic Algorithms for Protein Structure Prediction Using Low-Resolution Model
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient computation of fitness function by pruning in hydrophobic-hydrophilic model
ISBMDA'05 Proceedings of the 6th International conference on Biological and Medical Data Analysis
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We consider the problem of protein folding in the HP model on the two-dimensional square lattice. This problem is combinatorially equivalent to folding a string of 0's and 1's so that the string forms a self-avoiding walk on the lattice and the number of adjacent pairs of 1's is maximized. We present a linear-time 1/3-approximation algorithm for this problem, improving on the previous best approximation factor of 1/4. The approximation guarantee of this algorithm is based on an upper bound presented by Hart and Istrail [6] and used in all previous papers that address this problem. We show that this upper bound cannot be used to obtain an approximation factor better than 1/2.