RECOMB '97 Proceedings of the first annual international conference on Computational molecular biology
On the complexity of protein folding (extended abstract)
STOC '98 Proceedings of the thirtieth 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
A new algorithm for protein folding in the HP model
SODA '02 Proceedings of the thirteenth 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
Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices
ESA '99 Proceedings of the 7th Annual European Symposium on Algorithms
The algorithmics of folding proteins on lattices
Discrete Applied Mathematics - Special issue: Computational molecular biology series issue IV
Opportunities for Combinatorial Optimization in Computational Biology
INFORMS Journal on Computing
A Local Move Set for Protein Folding in Triangular Lattice Models
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
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The protein folding problem, i.e., the computational prediction of the three-dimensional structure of a protein from its amino acid sequence, is one of the most important and challenging problems in computational biology. Since a complete simulation of the folding process of a protein is far too complex to handle, one tries to find an approximate solution by using a simplified, abstract model. One of the most popular models is the so-called HP model, where the hydrophobic interactions between the amino acids are considered to be the main force in the folding process, and furthermore the folding space is modeled by a two- or three-dimensional grid lattice. In this paper, we will present some approximation algorithms for the protein folding problem in the HP model on an extended grid lattice with plane diagonals. The choice of this kind of lattice removes one of the major drawbacks of the original HP model, namely the bipartiteness of the grid which severely restricts the set of possible foldings. Our algorithms achieve an approximation ratio of 2615~1.733 for the two-dimensional and of 85=1.6 for the three-dimensional lattice. This improves significantly over the best previously known approximation ratios for the protein folding problem in the HP model on any lattice.