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3D Protein Structure Prediction with BSA-TS Algorithm

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Trends in Applied Knowledge-Based Systems and Data Science (IEA/AIE 2016)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 9799))

Abstract

Three-dimensional protein spatial structure prediction with the amino acid sequence can be converted to a global optimization problem of a multi-variable and multimodal function. This article uses an improved hybrid optimization algorithm named BSA-TS algorithm which combines Backtracking Search Optimization Algorithm (BSA) with Tabu Search (TS) Algorithm to predict the structure of protein based on the three-dimensional AB off-lattice model. It combines the advantage of BSA which has a simple and efficient algorithm framework, less control parameters and less sensitivity to the initial value of the control parameters and the advantage of TS which has a strong ability for the global neighborhood search, and can better overcome the shortcomings of traditional algorithms which have slow convergence rate and are easy to fall into local optimum. At last we experiment in some Fibonacci sequences and real protein sequences which are widely used in protein spatial structure prediction, and the experimental results show that the hybrid algorithm has good performance and accuracy.

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Acknowledgment

This work is supported by the National Natural Science Foundation of China (Nos. 61425002, 61402066, 61402067, 31370778, 61370005), Program for Changjiang Scholars and Innovative Research Team in University (No. IRT_15R07), the Program for Liaoning Innovative Research Team in University (No. LT2015002), the Basic Research Program of the Key Lab in Liaoning Province Educational Department (Nos. LZ2014049, LZ2015004), the Project Supported by Natural Science Foundation of Liaoning Province (No. 2014020132), and by the Project Supported by Scientific Research Fund of Liaoning Provincial Education (No. L2014499).

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Authors and Affiliations

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

    Yan Xu, Changjun Zhou, Qiang Zhang & Bin Wang

Authors
  1. Yan Xu
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  2. Changjun Zhou
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  3. Qiang Zhang
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  4. Bin Wang
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Corresponding author

Correspondence to Qiang Zhang .

Editor information

Editors and Affiliations

  1. Iwate Prefectural University , Iwate, Japan

    Hamido Fujita

  2. Department Computer Science, Texas State University, San Marcos, Texas, USA

    Moonis Ali

  3. Universiti Teknologi Malaysis (UTM), Bahru, Malaysia

    Ali Selamat

  4. Iwate Prefectural University , Iwate, Japan

    Jun Sasaki

  5. Iwate Prefectural University , Iwate, Japan

    Masaki Kurematsu

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Xu, Y., Zhou, C., Zhang, Q., Wang, B. (2016). 3D Protein Structure Prediction with BSA-TS Algorithm. In: Fujita, H., Ali, M., Selamat, A., Sasaki, J., Kurematsu, M. (eds) Trends in Applied Knowledge-Based Systems and Data Science. IEA/AIE 2016. Lecture Notes in Computer Science(), vol 9799. Springer, Cham. https://doi.org/10.1007/978-3-319-42007-3_38

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  • DOI: https://doi.org/10.1007/978-3-319-42007-3_38

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-42006-6

  • Online ISBN: 978-3-319-42007-3

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