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Improved hybrid optimization algorithm for 3D protein structure prediction

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Abstract

A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 31170797, 61103057, 31370778, 61370005), the Program for Changjiang Scholars and Innovative Research Team in University (No. IRT1109), the Key Project of Chinese Ministry of Education (No. 211036), the Project Supported by Scientific Research Fund of Liaoning Provincial Education Department (No. L2011218), the Project sponsored by "Liaoning BaiQianWan Talents Program" (No. 2013921007).

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Authors and Affiliations

  1. Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian, China

    Changjun Zhou, Caixia Hou, **aopeng Wei & Qiang Zhang

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  1. Changjun Zhou
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  2. Caixia Hou
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  3. **aopeng Wei
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  4. Qiang Zhang
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Correspondence to Changjun Zhou.

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Zhou, C., Hou, C., Wei, X. et al. Improved hybrid optimization algorithm for 3D protein structure prediction. J Mol Model 20, 2289 (2014). https://doi.org/10.1007/s00894-014-2289-2

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  • DOI: https://doi.org/10.1007/s00894-014-2289-2

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