QUATgo: Protein quaternary structural attributes predicted by two-stage machine learning approaches with heterogeneous feature encoding

• Published in: PloS one Vol. 15; no. 4; p. e0232087
• Main Authors: Tung, Chi-Hua, Chien, Ching-Hsuan, Chen, Chi-Wei, Huang, Lan-Ying, Liu, Yu-Nan, Chu, Yen-Wei
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 29.04.2020; Public Library of Science (PLoS)
• Subjects: Accuracy; Agricultural biotechnology; Algorithms; Amino acids; Bioinformatics; Biology and Life Sciences; Case studies; Coding; Composition; Computational biology; Computer applications; Datasets; Genomics; Hemagglutinins; Influenza; Influenza viruses; Internet; Learning algorithms; Lectins; Machine learning; Methods; Oligomers; Peptides; Physical Sciences; Principal components analysis; Protein structure; Proteins; Proteomics; Quaternary structure; Research and Analysis Methods; Servers; Support vector machines; Time; Viruses; Wavelet transforms; Web sites (World Wide Web); Taiwan
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0232087

Many proteins exist in natures as oligomers with various quaternary structural attributes rather than as single chains. Predicting these attributes is an essential task in computational biology for the advancement of proteomics. However, the existing methods do not consider the integration of heterogeneous coding and the accuracy of subunit categories with limited data. To this end, we proposed a tool that can predict more than 12 subunit protein oligomers, QUATgo. Meanwhile, three kinds of sequence coding were used, including dipeptide composition, which was used for the first time to predict protein quaternary structural attributes, and protein half-life characteristics, and we modified the coding method of the functional domain composition proposed by predecessors to solve the problem of large feature vectors. QUATgo solves the problem of insufficient data for a single subunit using a two-stage architecture and uses 10-fold cross-validation to test the predictive accuracy of the classifier. QUATgo has 49.0% cross-validation accuracy and 31.1% independent test accuracy. In the case study, the accuracy of QUATgo can reach 61.5% for predicting the quaternary structure of influenza virus hemagglutinin proteins. Finally, QUATgo is freely accessible to the public as a web server via the site http://predictor.nchu.edu.tw/QUATgo.