A Local Move Set for Protein Folding in Triangular Lattice Models

Authors:
Hans-Joachim Böckenhauer;Abu Zafer Dayem Ullah;Leonidas Kapsokalivas;Kathleen Steinhöfel
Affiliations:
Department of Computer Science, ETH Zürich, Zurich, Switzerland CH-8092;Department of Computer Science, King's College London, London, UK WC2R 2LS;Department of Computer Science, King's College London, London, UK WC2R 2LS;Department of Computer Science, King's College London, London, UK WC2R 2LS
Venue:
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Year:
2008

Citing 5
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Abstract

The HP model is one of the most popular discretized models for the protein folding problem, i.e., for computationally predicting the three-dimensional structure of a protein from its amino acid sequence. This model considers the interactions between hydrophobic amino acids to be the driving force in the folding process. Thus, it distinguishes between polar and hydrophobic amino acids only and asks for an embedding of the amino acid sequence into a rectangular grid lattice which maximizes the number of neighboring pairs (contacts) of hydrophobic amino acids in the lattice.In this paper, we consider an HP-like model which uses a more appropriate grid structure, namely the 2D triangular grid and the face-centered cubic lattice in 3D. We consider a local-search approach for finding an optimal embedding. For defining the local-search neighborhood, we design a move set, the so-called pull moves, and prove its reversibility and completeness. We then use these moves for a tabu search algorithm which is experimentally shown to lead into optimum energy configurations and improve the current best results for several sequences in 2D and 3D.