| Protein folding in the 2D HP model (1999) | |||||||||||||||||
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Abstract | |||||||||||||||||
| We study folding algorithms in the two dimensional Hydrophobic-Hydrophilic model (2D HP model) for protein structure formation. We consider three generalizations of the best known approximation algorithm. We show that two of the generalizations do not improve the worst case approximation ratio. The third generalization seems to be better, and the analysis of its approximation ratio leads to an interesting combinatorial problem. 1 Introduction Proteins are polymer chains of amino acids. An interesting feature of nature is that even though there are an innite amount of amino acids, only twenty dierent amino acids are used in the formation of proteins. The amino acid sequence of a protein can thus be abstracted as a string over an alphabet of size twenty. In nature proteins are of course not one dimensional strings but fold into three dimensional structures. The three dimensional structure of a protein is not static, but vibrates around an equilibrium known as the native state. Fa... | |||||||||||||||||
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