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 initio methods.
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Dotu, I., Cebrián, M., Van Hentenryck, P., Clote, P. (2008). Protein Structure Prediction with Large Neighborhood Constraint Programming Search. In: Stuckey, P.J. (eds) Principles and Practice of Constraint Programming. CP 2008. Lecture Notes in Computer Science, vol 5202. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-85958-1_6
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DOI: https://doi.org/10.1007/978-3-540-85958-1_6
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