Exact Enumeration of Three-Dimensional Lattice Proteins

TL;DR

This paper introduces an exact enumeration algorithm for all short 3D lattice proteins in the HP model, enabling comprehensive identification of designing sequences and contact maps for proteins up to 19 monomers.

Contribution

It provides a novel parallelized algorithm for exhaustive enumeration of 3D lattice proteins, facilitating complete analysis of their sequences and conformations.

Findings

Generated all contact maps for 3D lattice proteins up to 19 monomers.

Identified all designing sequences within the specified size range.

Demonstrated the effectiveness of parallel computing for exhaustive enumeration.

Abstract

We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing sequences of HP proteins consisting of up to 19 monomers whose conformations are represented by interacting self-avoiding walks on the simple cubic lattice. Employing a parallelized implementation on a Linux cluster, we generate the complete set of contact maps of such walks.