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

TL;DR

This paper introduces an equivalence relation on lattice protein structures in the HP model to efficiently enumerate optimal structures, reducing complexity in studying protein folding and design.

Contribution

It proposes a novel equivalence relation for optimal structures in the HP model and discusses methods for efficient enumeration of these classes.

Findings

Efficient enumeration of equivalence classes of optimal structures

Reduction in complexity for analyzing protein structures

Potential applications in protein design and analysis

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.