Protein structure prediction on the face centered cubic lattice by local search

Authors:
Manuel Cebrián;Ivan Dotú;Pascal Van Hentenryck;Peter Clote
Affiliations:
Department of Computer Science, Brown University, Providence, RI;Department of Computer Science, Brown University, Providence, RI;Department of Computer Science, Brown University, Providence, RI;Biology Department, Boston College, Chestnut Hill, MA
Venue:
AAAI'08 Proceedings of the 23rd national conference on Artificial intelligence - Volume 1
Year:
2008

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Abstract

Ab initio protein structure prediction is an important problem for which several algorithms have been developed. Algorithms differ by how they represent 3D protein conformations (on-lattice, off-lattice, coarse-grain or fine-grain model), by the energy model they consider, and whether they are heuristic or exact algorithms. This paper presents a local search algorithm to find the native state for the Hydrophobic-Polar (HP) model on the Face Centered Cubic (FCC) lattice; i.e. a self-avoiding walk on the FCC lattice with maximum number of H-H contacts. The algorithm relies on a randomized, structured initialization, a novel fitness function to guide the search, and efficient data structures to obtain self-avoiding walks. Experimental results on benchmark instances show the efficiency and excellent performance of our algorithm, and illustrate the biological pertinence of the FCC lattice.