An Improved Harmony Search Algorithm for Protein Structure Prediction Using 3D Off-Lattice Model

Protein structure prediction (PSP) is an important research area in bio-informatics for its immense scope of application in drug design, disease prediction, name a few. Structure prediction of protein based on sequence of amino acids is a NP-hard and multi-modal optimization problem. This paper presents an improved harmony search (ImHS) algorithm to solve the PSP problem based on 3D off lattice model. In the proposed method, the basic harmony search (HS) algorithm combined with dimensional mean based perturbation strategy to avoid premature convergence and enhance the capability of jumping out from the local optima. The experiments are carried out on a set of real protein sequences with different length collected from the Protein Data Bank (PDB) to validate the efficiency of the proposed method. Numerical results show that the ImHS algorithm significantly outperforms compared to other algorithms on protein energy minimization.

[1]  Zong Woo Geem,et al.  A New Heuristic Optimization Algorithm: Harmony Search , 2001, Simul..

[2]  Jesús S. Dehesa,et al.  Insight into the informational-structure behavior of the Diels-Alder reaction of cyclopentadiene and maleic anhydride , 2014, Journal of Molecular Modeling.

[3]  Changjun Zhou,et al.  Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm , 2015, Journal of Molecular Modeling.

[4]  Anurag Bagaria,et al.  Estimating structure quality trends in the Protein Data Bank by equivalent resolution , 2013, Comput. Biol. Chem..

[5]  Luís C. Lamb,et al.  Three-dimensional protein structure prediction: Methods and computational strategies , 2014, Comput. Biol. Chem..

[6]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[7]  Head-Gordon,et al.  Toy model for protein folding. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[8]  Yang Wang,et al.  Chaotic Artificial Bee Colony algorithm: A new approach to the problem of minimization of energy of the 3D protein structure , 2013, Molecular Biology.

[9]  Vitalii Lytvynov,et al.  A STUDY OF INTELLIGENT TECHNIQUES FOR PROTEIN SECONDARY STRUCTURE PREDICTION , 2015 .

[10]  Jing-fang Zhang,et al.  An improved global-best harmony search algorithm for faster optimization , 2014, Expert Syst. Appl..

[11]  Kuldip K. Paliwal,et al.  A Segmentation-Based Method to Extract Structural and Evolutionary Features for Protein Fold Recognition , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[12]  Rafael S. Parpinelli,et al.  Performance Analysis of Swarm Intelligence Algorithms for the 3D-AB off-lattice Protein Folding Problem , 2014, J. Multiple Valued Log. Soft Comput..

[13]  Francisco Herrera,et al.  A practical tutorial on the use of nonparametric statistical tests as a methodology for comparing evolutionary and swarm intelligence algorithms , 2011, Swarm Evol. Comput..

[14]  A. B. Dariane,et al.  Performance evaluation of an improved harmony search algorithm for numerical optimization: Melody Search (MS) , 2013, Eng. Appl. Artif. Intell..

[15]  Xiaolong Zhang,et al.  Protein structure prediction with local adjust tabu search algorithm , 2014, BMC Bioinformatics.

[16]  Swagatam Das,et al.  An improved particle swarm optimizer with difference mean based perturbation , 2014, Neurocomputing.

[17]  Heitor S. Lopes,et al.  An improved parallel differential evolution approach for protein structure prediction using both 2D and 3D off-lattice models , 2013, 2013 IEEE Symposium on Differential Evolution (SDE).

[18]  D. Mount.  Bioinformatics: Sequence and Genome Analysis , 2001 .

[19]  Raymond Chiong,et al.  A balance-evolution artificial bee colony algorithm for protein structure optimization based on a three-dimensional AB off-lattice model , 2015, Comput. Biol. Chem..

[20]  Jing J. Liang,et al.  Problem Definitions and Evaluation Criteria for the CEC 2005 Special Session on Real-Parameter Optimization , 2005 .

[21]  Tatyana E. Shubina,et al.  A topical collection on the occasion of Tim Clark’s 65th birthday , 2015, Journal of Molecular Modeling.

[22]  Pedro Alexandrino Fernandes,et al.  Protein–ligand docking: Current status and future challenges , 2006, Proteins.

[23]  Qiang Zhang,et al.  Improved hybrid optimization algorithm for 3D protein structure prediction , 2014, Journal of Molecular Modeling.