Non-Isomorphic Coding in Lattice Model and its Impact for Protein Folding Prediction Using Genetic Algorithm

Houqe, Tamjid; Chetty, Madhu and Dooley, Laurence S. (2006). Non-Isomorphic Coding in Lattice Model and its Impact for Protein Folding Prediction Using Genetic Algorithm. In: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB’06), 28-29 Sep 2006, Toronto.

DOI: https://doi.org/10.1109/CIBCB.2006.331014

URL: http://ieeexplore.ieee.org/search/wrapper.jsp?arnu...

Abstract

Traditional encodings for hydrophobic(H)-hydrophilic(P) model or HP lattice models is isomorphic, which adds unwanted variations for the same solution, thereby slowing convergence. In this paper a novel non-isomorphic encoding scheme is presented for HP lattice model, which constrains the search space. In addition, similarity comparisons are made easier and more consistent and it will be shown that non-deterministic search approach such as genetic algorithm (GA) converges faster when non-isomorphic encoding is employed.

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