Liu Q, Chen P, Wang B, Zhang J, Li J. Hot spot prediction in protein-protein interactions by an ensemble system.
BMC SYSTEMS BIOLOGY 2018;
12:132. [PMID:
30598091 PMCID:
PMC6311905 DOI:
10.1186/s12918-018-0665-8]
[Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND
Hot spot residues are functional sites in protein interaction interfaces. The identification of hot spot residues is time-consuming and laborious using experimental methods. In order to address the issue, many computational methods have been developed to predict hot spot residues. Moreover, most prediction methods are based on structural features, sequence characteristics, and/or other protein features.
RESULTS
This paper proposed an ensemble learning method to predict hot spot residues that only uses sequence features and the relative accessible surface area of amino acid sequences. In this work, a novel feature selection technique was developed, an auto-correlation function combined with a sliding window technique was applied to obtain the characteristics of amino acid residues in protein sequence, and an ensemble classifier with SVM and KNN base classifiers was built to achieve the best classification performance.
CONCLUSION
The experimental results showed that our model yields the highest F1 score of 0.92 and an MCC value of 0.87 on ASEdb dataset. Compared with other machine learning methods, our model achieves a big improvement in hot spot prediction.
AVAILABILITY
http://deeplearner.ahu.edu.cn/web/HotspotEL.htm .
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