Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains - Computer Science > Computational Engineering, Finance, and ScienceReport as inadecuate




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Abstract: Lattice protein models, as the Hydrophobic-Polar HP model, are a commonabstraction to enable exhaustive studies on structure, function, or evolutionof proteins. A main issue is the high number of optimal structures, resultingfrom the hydrophobicity-based energy function applied. We introduce anequivalence relation on protein structures that correlates to the energyfunction. We discuss the efficient enumeration of optimal representatives ofthe corresponding equivalence classes and the application of the results.



Author: Martin Mann, Rolf Backofen, Sebastian Will

Source: https://arxiv.org/







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