Developing Computational Model to Predict Protein-Protein Interaction Sites Based on the XGBoost Algorithm

Deng, Aijun; Zhang, Huan; Wang, Wenyan; Zhang, Jun; Fan, Dingdong; Chen, Peng; Wang, Bing

doi:10.3390/ijms21072274

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Developing Computational Model to Predict Protein-Protein Interaction Sites Based on the XGBoost Algorithm

^1,2,3,†,

^4,†,

⁴,

⁵,

²,

^5,*

and

Bing Wang

^1,4,5,*

Key Laboratory of Metallurgical Emission Reduction & Resources Recycling (Anhui University of Technology), Ministry of Education, Ma’anshan 243002, China

School of Metallurgical Engineering, Anhui University of Technology, Ma’anshan 243032, China

Department of Engineering, University of Leicester, Leicester LE1 7RH, UK

⁴

School of Electrical and Information Engineering, Anhui University of Technology, Ma’anshan 243032, China

⁵

Co-Innovation Center for Information Supply & Assurance Technology, Anhui University, Hefei 230032, China

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Int. J. Mol. Sci. 2020, 21(7), 2274; https://doi.org/10.3390/ijms21072274

Received: 3 February 2020 / Revised: 10 March 2020 / Accepted: 23 March 2020 / Published: 25 March 2020

(This article belongs to the Special Issue Recent Advances in Biomolecular Recognition)

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Abstract

The study of protein-protein interaction is of great biological significance, and the prediction of protein-protein interaction sites can promote the understanding of cell biological activity and will be helpful for drug development. However, uneven distribution between interaction and non-interaction sites is common because only a small number of protein interactions have been confirmed by experimental techniques, which greatly affects the predictive capability of computational methods. In this work, two imbalanced data processing strategies based on XGBoost algorithm were proposed to re-balance the original dataset from inherent relationship between positive and negative samples for the prediction of protein-protein interaction sites. Herein, a feature extraction method was applied to represent the protein interaction sites based on evolutionary conservatism of proteins, and the influence of overlapping regions of positive and negative samples was considered in prediction performance. Our method showed good prediction performance, such as prediction accuracy of 0.807 and MCC of 0.614, on an original dataset with 10,455 surface residues but only 2297 interface residues. Experimental results demonstrated the effectiveness of our XGBoost-based method. View Full-Text

Keywords: protein interaction sites; unbalanced data sets; overlapping regions; XGBoost

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MDPI and ACS Style

Deng, A.; Zhang, H.; Wang, W.; Zhang, J.; Fan, D.; Chen, P.; Wang, B. Developing Computational Model to Predict Protein-Protein Interaction Sites Based on the XGBoost Algorithm. Int. J. Mol. Sci. 2020, 21, 2274. https://doi.org/10.3390/ijms21072274

AMA Style

Deng A, Zhang H, Wang W, Zhang J, Fan D, Chen P, Wang B. Developing Computational Model to Predict Protein-Protein Interaction Sites Based on the XGBoost Algorithm. International Journal of Molecular Sciences. 2020; 21(7):2274. https://doi.org/10.3390/ijms21072274

Chicago/Turabian Style

Deng, Aijun, Huan Zhang, Wenyan Wang, Jun Zhang, Dingdong Fan, Peng Chen, and Bing Wang. 2020. "Developing Computational Model to Predict Protein-Protein Interaction Sites Based on the XGBoost Algorithm" International Journal of Molecular Sciences 21, no. 7: 2274. https://doi.org/10.3390/ijms21072274

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