Lattice model refinement of protein structures

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.

In Proceedings of Workshop on Constraint Based Methods for Bioinformatics (WCB 2010); Jul 21, 2010; Edinburgh, UK (co-located with ICLP 2010); 7 pages