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A Novel Index of Contact Frequency from Noise Protein–Protein Interaction Data Help for Accurate Interface Residue Pair Prediction

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Abstract

Protein–protein interactions are important for most biological processes and have been studied for decades. However, the detailed formation mechanism of protein–protein interaction interface is still ambiguous, which makes it difficult to accurately predict the protein–protein interaction interface residue pairs. Here, we extract the interface residue–residue contacts from the decoys in the ZDOCK protein–protein complex decoy set with RMSD mostly larger than 3 Å. To accurately compute the interface residue–residue contacts, we define a new constant called interface residue pairs frequency, which counts the atom contact numbers between two interface residues. We normalize interface residue pairs frequency to pick out the top residue–residue pairs from all the possible pairs preferential to be on correct protein–protein interaction interface. When tested on 37 protein dimers from the decoy set where most decoys are incorrect, our method successfully predicts 30 protein dimers with a success rate of up to 81.1%. Higher accuracy than some other state-of-the-art methods confirmed the performance of our method.

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Acknowledgements

This paper has been accepted by CBC2019. We thank the CBC2019 reviewers. This research was supported by the National Natural Science Foundation of China (31670725) and Beijing Advanced Structural Biology Center of Tsinghua University, the Fundamental Research Funds for the Central Universities, and the Research Funds of Renmin University of China.

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Authors and Affiliations

  1. Mathematical Intelligence Application Lab, Institute for Mathematical Sciences, School of Math, Renmin University of China, Beijing, 100872, China

    Yanfen Lyu, He Huang & Xinqi Gong

Authors
  1. Yanfen Lyu
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  2. He Huang
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  3. Xinqi Gong
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Contributions

YFL developed the algorithm, did the computation, and wrote the initial manuscript. HH helped to write data analysis code and data processing. XQG designed the project, collected the data and revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Xinqi Gong.

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The author states that the present manuscript presents no conflict of interest.

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Lyu, Y., Huang, H. & Gong, X. A Novel Index of Contact Frequency from Noise Protein–Protein Interaction Data Help for Accurate Interface Residue Pair Prediction. Interdiscip Sci Comput Life Sci 12, 204–216 (2020). https://doi.org/10.1007/s12539-020-00364-w

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