GPS 2.0, a Tool to Predict Kinase-specific Phosphorylation Sites in Hierarchy *S
By Yu Xue, Jian Ren, Xinjiao Gao, Changjiang Jin, Long‐ping Wen, X. Yao. Molecular & Cellular Proteomics, 2008
662 citations recorded by the source corpus.
Identification of protein phosphorylation sites with their cognate protein kinases (PKs) is a key step to delineate molecular dynamics and plasticity underlying a variety of cellular processes. Although nearly 10 kinase-specific prediction programs have been developed, numerous PKs have been casually classified into subgroups without a standard rule. For large scale predictions, the false positive rate has also never been addressed. In this work, we adopted a well established rule to classify PKs into a hierarchical structure with four levels, including group, family, subfamily, and single PK. In addition, we developed a simple approach to estimate the theoretically maximal false positive rates. The on-line service and local packages of the GPS (Group-based Prediction System) 2.0 were implemented in Java with the modified version of the Group-based Phosphorylation Scoring algorithm. As the first stand alone software for predicting phosphorylation, GPS 2.0 can predict kinase-specific phosphorylation sites for 408 human PKs in hierarchy. A large scale prediction of more than 13,000 mammalian phosphorylation sites by GPS 2.0 was exhibited with great performance and remarkable accuracy. Using Aurora-B as an example, we also conducted a proteome-wide search and provided systematic prediction of Aurora-B-specific substrates including protein-protein interaction information. Thus, the GPS 2.0 is a useful tool for predicting protein phosphorylation sites and their cognate kinases and is freely available on line.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/2f7c168428706bc57e4835d466c0589ea6d3b7ed
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- PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction (2018, methodology): “3), and the area under the ROC curve (AUC) 9 .”
- Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells (2012, background): “Computational analysis predicts that the Src kinase may be responsible for the Tyr 18 phosphorylation of FUNDC1 (refs&nbs”