Protein Structure Prediction with Large Neighborhood Constraint Programming Search

Authors:
Ivan Dotu;Manuel Cebrián;Pascal Hentenryck;Peter Clote
Affiliations:
Department of Computer Science, Brown University, Providence, RI 02912;Department of Computer Science, Brown University, Providence, RI 02912;Department of Computer Science, Brown University, Providence, RI 02912;Biology Department, Boston College, Chestnut Hill, MA 02467
Venue:
CP '08 Proceedings of the 14th international conference on Principles and Practice of Constraint Programming
Year:
2008

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Abstract

Protein structure predictions is regarded as a highly challenging problem both for the biology and for the computational communities. Many approaches have been developed in the recent years, moving to increasingly complex lattice models or even off-lattice models. This paper presents a Large Neighborhood Search (LNS) to find the native state for the Hydrophobic-Polar (HP) model on the Face Centered Cubic (FCC) lattice or, in other words, a self- avoiding walk on the FCC lattice having a maximum number of H-H contacts. The algorithm starts with a tabu-search algorithm, whose solution is then improved by a combination of constraint programming and LNS. This hybrid algorithm improves earlier approaches in the literature over several well-known instances and demonstrates the potential of constraint-programming approaches for ab initiomethods.