Lattice model refinement of protein structures

TL;DR

This paper introduces a constraint programming approach to refine lattice models of protein structures, improving quality over previous greedy methods, with promising extensions discussed.

Contribution

It presents a novel constraint programming method for lattice model refinement of proteins, outperforming biased greedy approaches.

Findings

Better quality lattice models achieved

Prototype implemented in COLA with limited discrepancy search

Extensions with local search are promising

Abstract

To find the best lattice model representation of a given full atom protein structure is a hard computational problem. Several greedy methods have been suggested where results are usually biased and leave room for improvement. In this paper we formulate and implement a Constraint Programming method to refine such lattice structure models. We show that the approach is able to provide better quality solutions. The prototype is implemented in COLA and is based on limited discrepancy search. Finally, some promising extensions based on local search are discussed.