Memory-based local search for simplified protein structure prediction

Authors:
Swakkhar Shatabda;M. A. Hakim Newton;Duc Nghia Pham;Abdul Sattar
Affiliations:
Griffith University;Griffith University;Griffith University;Griffith University
Venue:
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Year:
2012

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Abstract

Protein structure prediction is one of the most challenging problems in computational biology. Given a protein's amino acid sequence, a simplified version of the problem is to find an on-lattice self-avoiding walk that minimizes the interaction energy among the amino acids. In this paper, we present a memory-based local search method for the simplified problem using Hydrophobic-Polar energy model and Face Centered Cubic lattice. By memorizing local minima and then avoiding their neighbohood, our approach significantly improves the state-of-the-art local search method for protein structure prediction on a set of standard benchmark proteins.