中国物理B ›› 2020, Vol. 29 ›› Issue (10): 108707-.doi: 10.1088/1674-1056/abb659

所属专题: SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids

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Daiwen Sun(孙黛雯)1, Shijie Liu(刘世婕)1, Xinqi Gong(龚新奇)1,2,†()   

  • 收稿日期:2020-06-29 修回日期:2020-08-31 接受日期:2020-09-09 出版日期:2020-10-05 发布日期:2020-10-05
  • 通讯作者: Xinqi Gong(龚新奇)

Review of multimer protein–protein interaction complex topology and structure prediction

Daiwen Sun(孙黛雯)1, Shijie Liu(刘世婕)1, and Xinqi Gong(龚新奇)1,2,†   

  1. 1 Mathematics Intelligence Application Laboratory, Institute for Mathematical Sciences, Renmin University of China, Beijing 100872, China
    2 Beijing Advanced Innovation Center for Structural Biology, Tshinghua University, Beijing 100094, China
  • Received:2020-06-29 Revised:2020-08-31 Accepted:2020-09-09 Online:2020-10-05 Published:2020-10-05
  • Contact: Corresponding author. E-mail: xinqigong@ruc.edu.cn
  • About author:
    †Corresponding author. E-mail: xinqigong@ruc.edu.cn
    * Project supported by the National Natural Science Foundation of China (Grant No. 31670725).

Abstract:

Protein–protein interactions (PPI) are important for many biological processes. Theoretical understanding of the structurally determining factors of interaction sites will help to understand the underlying mechanism of protein–protein interactions. At the same time, understanding the complex structure of proteins helps to explore their function. And accurately predicting protein complexes from PPI networks helps us understand the relationship between proteins. In the past few decades, scholars have proposed many methods for predicting protein interactions and protein complex structures. In this review, we first briefly introduce the methods and servers for predicting protein interaction sites and interface residue pairs, and then introduce the protein complex structure prediction methods including template-based prediction and template-free prediction. Subsequently, this paper introduces the methods of predicting protein complexes from the PPI network and the method of predicting missing links in the PPI network. Finally, it briefly summarizes the application of machine/deep learning models in protein structure prediction and action site prediction.

Key words: protein complex prediction, protein-protein interaction

中图分类号:  (Protein-protein interactions)

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