Projects per year
Abstract
Motivation: Kinase-regulated phosphorylation is a ubiquitous type of post-translational modification (PTM) in both eukaryotic and prokaryotic cells. Phosphorylation plays fundamental roles in many signalling pathways and biological processes, such as protein degradation and protein-protein interactions. Experimental studies have revealed that signalling defects caused by aberrant phosphorylation are highly associated with a variety of human diseases, especially cancers. In light of this, a number of computational methods aiming to accurately predict protein kinase family-specific or kinase-specific phosphorylation sites have been established, thereby facilitating phosphoproteomic data analysis. Results: In this work, we present Quokka, a novel bioinformatics tool that allows users to rapidly and accurately identify human kinase family-regulated phosphorylation sites. Quokka was developed by using a variety of sequence scoring functions combined with an optimized logistic regression algorithm. We evaluated Quokka based on well-prepared up-to-date benchmark and independent test datasets, curated from the Phospho.ELM and UniProt databases, respectively. The independent test demonstrates that Quokka improves the prediction performance compared with state-of-the-art computational tools for phosphorylation prediction. In summary, our tool provides users with high-quality predicted human phosphorylation sites for hypothesis generation and biological validation. Availability and implementation: The Quokka webserver and datasets are freely available at http://quokka.erc.monash.edu/. Supplementary information: Supplementary data are available at Bioinformatics online.
Original language | English |
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Article number | bty522 |
Pages (from-to) | 4223-4231 |
Number of pages | 9 |
Journal | Bioinformatics |
Volume | 34 |
Issue number | 24 |
DOIs | |
Publication status | Published - 15 Dec 2018 |
Projects
- 3 Finished
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Stochastic modelling of telomere length regulation in ageing research
Australian Research Council (ARC), Monash University
3/01/12 → 30/10/17
Project: Research
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Characterisation of plant cysteine proteases with therapeutic potential
Pike, R., Song, J., Whisstock, J. & Mynott, T.
Australian Research Council (ARC), Sarantis Limited
1/07/11 → 30/06/14
Project: Research
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NHMRC Research Fellowship
National Health and Medical Research Council (NHMRC) (Australia)
1/01/09 → 31/12/19
Project: Research
Press/Media
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Bioinformatics tool to unearth new pointers to disease
10/07/18
1 item of Media coverage
Press/Media: Research
Equipment
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Australian Synchrotron
Office of the Vice-Provost (Research and Research Infrastructure)Facility/equipment: Facility