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A Firefly-Inspired Method for Protein Structure Prediction in Lattice Models
Department of Informatics, King's College London, Strand, London WC2R 2LS, UK
School of Science and Technology, Middlesex University, The Burroughs, London, NW4 4BT, UK
* Author to whom correspondence should be addressed.
Received: 1 December 2013; in revised form: 17 December 2013 / Accepted: 27 December 2013 / Published: 7 January 2014
Abstract: We introduce a Firefly-inspired algorithmic approach for protein structure prediction over two different lattice models in three-dimensional space. In particular, we consider three-dimensional cubic and three-dimensional face-centred-cubic (FCC) lattices. The underlying energy models are the Hydrophobic-Polar (H-P) model, the Miyazawa–Jernigan (M-J) model and a related matrix model. The implementation of our approach is tested on ten H-P benchmark problems of a length of 48 and ten M-J benchmark problems of a length ranging from 48 until 61. The key complexity parameter we investigate is the total number of objective function evaluations required to achieve the optimum energy values for the H-P model or competitive results in comparison to published values for the M-J model. For H-P instances and cubic lattices, where data for comparison are available, we obtain an average speed-up over eight instances of 2.1, leaving out two extreme values (otherwise, 8.8). For six M-J instances, data for comparison are available for cubic lattices and runs with a population size of 100, where, a priori, the minimum free energy is a termination criterion. The average speed-up over four instances is 1.2 (leaving out two extreme values, otherwise 1.1), which is achieved for a population size of only eight instances. The present study is a test case with initial results for ad hoc parameter settings, with the aim of justifying future research on larger instances within lattice model settings, eventually leading to the ultimate goal of implementations for off-lattice models.
Keywords: protein folding; lattice models; H-P and M-J energy functions; Firefly Algorithm
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Maher, B.; Albrecht, A.A.; Loomes, M.; Yang, X.-S.; Steinhöfel, K. A Firefly-Inspired Method for Protein Structure Prediction in Lattice Models. Biomolecules 2014, 4, 56-75.
Maher B, Albrecht AA, Loomes M, Yang X-S, Steinhöfel K. A Firefly-Inspired Method for Protein Structure Prediction in Lattice Models. Biomolecules. 2014; 4(1):56-75.
Maher, Brian; Albrecht, Andreas A.; Loomes, Martin; Yang, Xin-She; Steinhöfel, Kathleen. 2014. "A Firefly-Inspired Method for Protein Structure Prediction in Lattice Models." Biomolecules 4, no. 1: 56-75.