Improve hot region prediction by analyzing different machine learning algorithms

BMC Bioinformatics

Nansheng Chen¹  Jing Hu²  Xiaolong Zhang²  Bo Li²  Longwei Zhou² 

[1] Molecular Biology and Biochemistry, Simon Fraser University;School of Computer Science and Technology, Wuhan University of Science and Technology;

关键词: Hot region;    Protein–protein interaction;    Hot spot;    DBSCAN;    SVM;    Gaussian Naïve Bayes;   

DOI  :  10.1186/s12859-021-04420-0

来源: DOAJ

【 摘 要 】

Abstract Background In the process of designing drugs and proteins, it is crucial to recognize hot regions in protein–protein interactions. Each hot region of protein–protein interaction is composed of at least three hot spots, which play an important role in binding. However, it takes time and labor force to identify hot spots through biological experiments. If predictive models based on machine learning methods can be trained, the drug design process can be effectively accelerated. Results The results show that different machine learning algorithms perform similarly, as evaluating using the F-measure. The main differences between these methods are recall and precision. Since the key attribute of hot regions is that they are packed tightly, we used the cluster algorithm to predict hot regions. By combining Gaussian Naïve Bayes and DBSCAN, the F-measure of hot region prediction can reach 0.809. Conclusions In this paper, different machine learning models such as Gaussian Naïve Bayes, SVM, Xgboost, Random Forest, and Artificial Neural Network are used to predict hot spots. The experiment results show that the combination of hot spot classification algorithm with higher recall rate and clustering algorithm with higher precision can effectively improve the accuracy of hot region prediction.

【 授权许可】

Unknown