THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model.

Journal: Bioinformatics (Oxford, England)
PMID: 37874953

Abstract

MOTIVATION: Quantitative determination of protein thermodynamic stability is a critical step in protein and drug design. Reliable prediction of protein stability changes caused by point variations contributes to developing-related fields. Over the past decades, dozens of structure-based and sequence-based methods have been proposed, showing good prediction performance. Despite the impressive progress, it is necessary to explore wild-type and variant protein representations to address the problem of how to represent the protein stability change in view of global sequence. With the development of structure prediction using learning-based methods, protein language models (PLMs) have shown accurate and high-quality predictions of protein structure. Because PLM captures the atomic-level structural information, it can help to understand how single-point variations cause functional changes.

Authors

  • Jianting Gong
    School of Information Science and Technology, Institution of Computational Biology, Northeast Normal University, Changchun 130117, China.
  • Lili Jiang
    Department of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
  • Yongbing Chen
    School of Information Science and Technology, Northeast Normal University, Changchun, China.
  • Yixiang Zhang
    Weifang Medical University, Weifang, China.
  • Xue Li
    Department of Clinical Research Center, Dazhou Central Hospital, Dazhou 635000, China.
  • Zhiqiang Ma
    Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China. Electronic address: zhiqiang.ma967@gmail.com.
  • Zhiguo Fu
    School of Information Science and Technology, Institution of Computational Biology, Northeast Normal University, Changchun 130117, China.
  • Fei He
    Biology Department, Brookhaven National Laboratory, Upton, New York, USA.
  • Pingping Sun
    School of Information Science and Technology, Northeast Normal University, Changchun 130117, China.
  • Zilin Ren
    Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
  • Mingyao Tian
    Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.

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