Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains

Details Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains

2009-10-20

arxiv.org/abs/0910.3848v1

In Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009, Lisbon

Computer Science

Computational Engineering, Finance, and Science

Published in Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009, 9 pages

Scientific paper

Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the hydrophobicity-based energy function applied. We introduce an equivalence relation on protein structures that correlates to the energy function. We discuss the efficient enumeration of optimal representatives of the corresponding equivalence classes and the application of the results.

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