Zhao M-XDing R-FChen QMeng JLi FFu SHuang BLiu YJi Z-LZhao YXue Y2024-11-062024-11-062024-04-10Zhao M-X, Ding R-F, Chen Q, Meng J, Li F, Fu S, Huang B, Liu Y, Ji Z-L, Zhao Y. (2024). Nphos: Database and Predictor of Protein N-phosphorylation.. Genomics Proteomics Bioinformatics. 22. 3. (pp. qzae032-).1672-0229https://mro.massey.ac.nz/handle/10179/71933Protein N-phosphorylation is widely present in nature and participates in various biological processes. However, current knowledge on N-phosphorylation is extremely limited compared to that on O-phosphorylation. In this study, we collected 11,710 experimentally verified N-phosphosites of 7344 proteins from 39 species and subsequently constructed the database Nphos to share up-to-date information on protein N-phosphorylation. Upon these substantial data, we characterized the sequential and structural features of protein N-phosphorylation. Moreover, after comparing hundreds of learning models, we chose and optimized gradient boosting decision tree (GBDT) models to predict three types of human N-phosphorylation, achieving mean area under the receiver operating characteristic curve (AUC) values of 90.56%, 91.24%, and 92.01% for pHis, pLys, and pArg, respectively. Meanwhile, we discovered 488,825 distinct N-phosphosites in the human proteome. The models were also deployed in Nphos for interactive N-phosphosite prediction. In summary, this work provides new insights and points for both flexible and focused investigations of N-phosphorylation. It will also facilitate a deeper and more systematic understanding of protein N-phosphorylation modification by providing a data and technical foundation. Nphos is freely available at http://www.bio-add.org/Nphos/ and http://ppodd.org.cn/Nphos/.(c) 2024 The Author/sCC BY 4.0https://creativecommons.org/licenses/by/4.0/N-phosphorylationBenchmark datasetDatabaseMachine learningPost-translational modificationPhosphorylationDatabases, ProteinHumansPhosphoproteinsProteomeJournal article10.1093/gpbjnl/qzae0322210-3244journal-articleqzae032-https://www.ncbi.nlm.nih.gov/pubmed/39380205qzae0327643521