Artificial intelligence-based multi-objective optimization protocol for protein structure refinement.

Journal: Bioinformatics (Oxford, England)
Published Date: Jan 15, 2020

Abstract

MOTIVATION: Protein structure refinement is an important step of protein structure prediction. Existing approaches have generally used a single scoring function combined with Monte Carlo method or Molecular Dynamics algorithm. The one-dimension optimization of a single energy function may take the structure too far away without a constraint. The basic motivation of our study is to reduce the bias problem caused by minimizing only a single energy function due to the very diversity of different protein structures.

Authors

  • Di Wang
    Center for Endocrine Metabolism and Immune Diseases, Beijing Luhe Hospital, Capital Medical University, Beijing, People's Republic of China.
  • Ling Geng
    Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
  • Yu-Jun Zhao
    School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, Jiangsu 21116, China.
  • Yang Yang
    Department of Gastrointestinal Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, China.
  • Yan Huang
    Department of Neurology, University of Texas Health Science Center at Houston, Houston, TX.
  • Yang Zhang
    Innovative Institute of Chinese Medicine and Pharmacy, Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
  • Hong-Bin Shen
    Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China. hbshen@sjtu.edu.cn.

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