Lattice model refinement of protein structures

Details Lattice model refinement of protein structures Lattice model refinement of protein structures

2010-05-10

arxiv.org/abs/1005.1853v1

Computer Science

Computational Engineering, Finance, and Science

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

Scientific paper

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.

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