Ubiquinone is an important cofactor that plays vital and diverse roles in many biological processes. Ubiquinone-binding proteins (UBPs) are receptor proteins that dock with ubiquinones. Analyzing and identifying UBPs via a computational approach will provide insights into the pathways associated with ubiquinones. In this work, we were the first to propose a UBPs predictor (UBPs-Pred). The optimal feature subset selected from three categories of sequence-derived features was fed into the extreme gradient boosting (XGBoost) classifier, and the parameters of XGBoost were tuned by multi-objective particle swarm optimization (MOPSO). The experimental results over the independent validation demonstrated considerable prediction performance with a Matthews correlation coefficient (MCC) of 0.517. After that, we analyzed the UBPs using bioinformatics methods, including the statistics of the binding domain motifs and protein distribution, as well as an enrichment analysis of the gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway.
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