Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains
Computational Engineering, Finance, and Science
2009-10-21 v1 Biomolecules
Abstract
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.
Cite
@article{arxiv.0910.3848,
title = {Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains},
author = {Martin Mann and Rolf Backofen and Sebastian Will},
journal= {arXiv preprint arXiv:0910.3848},
year = {2009}
}
Comments
Published in Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009, 9 pages