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An improved stochastic fractal search algorithm for 3D protein structure prediction

  • Changjun ZhouEmail author
  • Chuan Sun
  • Bin Wang
  • Xiaojun Wang
Original Paper
  • 198 Downloads

Abstract

Protein structure prediction (PSP) is a significant area for biological information research, disease treatment, and drug development and so on. In this paper, three-dimensional structures of proteins are predicted based on the known amino acid sequences, and the structure prediction problem is transformed into a typical NP problem by an AB off-lattice model. This work applies a novel improved Stochastic Fractal Search algorithm (ISFS) to solve the problem. The Stochastic Fractal Search algorithm (SFS) is an effective evolutionary algorithm that performs well in exploring the search space but falls into local minimums sometimes. In order to avoid the weakness, Lvy flight and internal feedback information are introduced in ISFS. In the experimental process, simulations are conducted by ISFS algorithm on Fibonacci sequences and real peptide sequences. Experimental results prove that the ISFS performs more efficiently and robust in terms of finding the global minimum and avoiding getting stuck in local minimums.

Keywords

Protein structure prediction AB off-lattice model Stochastic fractal search algorithm Lvy flight Internal feedback information 

Notes

Acknowledgements

This work is supported by the National Natural Science Foundation of China (Nos. 61672121, 61751203, 61772100, 61702070, 61572093), 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 (No. LZ2015004).

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Changjun Zhou
    • 1
    Email author
  • Chuan Sun
    • 1
  • Bin Wang
    • 1
  • Xiaojun Wang
    • 1
  1. 1.Key Laboratory of Advanced Design and Intelligent Computing (Dalian University)Ministry of EducationDalianChina

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