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Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Author

Listed:
  • Zhiye Guo

    (University of Missouri)

  • Jian Liu

    (University of Missouri)

  • Jeffrey Skolnick

    (Georgia Institute of Technology)

  • Jianlin Cheng

    (University of Missouri)

Abstract

Residue-residue distance information is useful for predicting tertiary structures of protein monomers or quaternary structures of protein complexes. Many deep learning methods have been developed to predict intra-chain residue-residue distances of monomers accurately, but few methods can accurately predict inter-chain residue-residue distances of complexes. We develop a deep learning method CDPred (i.e., Complex Distance Prediction) based on the 2D attention-powered residual network to address the gap. Tested on two homodimer datasets, CDPred achieves the precision of 60.94% and 42.93% for top L/5 inter-chain contact predictions (L: length of the monomer in homodimer), respectively, substantially higher than DeepHomo’s 37.40% and 23.08% and GLINTER’s 48.09% and 36.74%. Tested on the two heterodimer datasets, the top Ls/5 inter-chain contact prediction precision (Ls: length of the shorter monomer in heterodimer) of CDPred is 47.59% and 22.87% respectively, surpassing GLINTER’s 23.24% and 13.49%. Moreover, the prediction of CDPred is complementary with that of AlphaFold2-multimer.

Suggested Citation

  • Zhiye Guo & Jian Liu & Jeffrey Skolnick & Jianlin Cheng, 2022. "Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34600-2
    DOI: 10.1038/s41467-022-34600-2
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    References listed on IDEAS

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    1. Sheng Wang & Siqi Sun & Zhen Li & Renyu Zhang & Jinbo Xu, 2017. "Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model," PLOS Computational Biology, Public Library of Science, vol. 13(1), pages 1-34, January.
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    Cited by:

    1. Peicong Lin & Yumeng Yan & Huanyu Tao & Sheng-You Huang, 2023. "Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Jiahua Rao & Jiancong Xie & Qianmu Yuan & Deqin Liu & Zhen Wang & Yutong Lu & Shuangjia Zheng & Yuedong Yang, 2024. "A variational expectation-maximization framework for balanced multi-scale learning of protein and drug interactions," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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