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Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources

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Plant Phosphoproteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2358))

Abstract

Most proteins undergo some form of modification after translation, and phosphorylation is one of the most relevant and ubiquitous post-translational modifications. The succession of protein phosphorylation and dephosphorylation catalyzed by protein kinase and phosphatase, respectively, constitutes a key mechanism of molecular information flow in cellular systems. The protein interactions of kinases, phosphatases, and their regulatory subunits and substrates are the main part of phosphorylation networks. To elucidate the landscape of phosphorylation events has been a central goal pursued by both experimental and computational approaches. Substrate specificity (e.g., sequence, structure) or the phosphoproteome has been utilized in an array of different statistical learning methods to infer phosphorylation networks. In this chapter, different computational phosphorylation network inference-related methods and resources are summarized and discussed.

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Authors and Affiliations

  1. Department of Neurology, The First Affiliated Hospital of Shandong First Medical University, Jinan, People’s Republic of China

    Min Zhang

  2. Energy Plant Research Center, School of Life Sciences, Qilu Normal University, Jinan, People’s Republic of China

    Guangyou Duan

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  1. Min Zhang
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  2. Guangyou Duan
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Correspondence to Guangyou Duan .

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  1. State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China

    Xu Na Wu

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Zhang, M., Duan, G. (2021). Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources. In: Wu, X.N. (eds) Plant Phosphoproteomics. Methods in Molecular Biology, vol 2358. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1625-3_15

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  • DOI: https://doi.org/10.1007/978-1-0716-1625-3_15

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  • Online ISBN: 978-1-0716-1625-3

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