From phosphosites to kinases

Methods in Molecular Biology

Volumn 1355, Issue , 2016, Pages 307-321

  Munk, Stephanie ^a   Refsgaard, Jan C ^a   Olsen, Jesper V ^a   Jensen, Lars J ^a  

^a NONE

Author keywords

Kinases; NetPhorest; NetworKIN; PhoshoSitePlus; PHOSIDA; Phospho.ELM; Phosphoproteomics

Indexed keywords

PHOSPHOTRANSFERASE; PHOSPHOPROTEIN; PROTEIN KINASE;

BIOINFORMATICS; CHEMICAL DATABASE; CONSENSUS SEQUENCE; PROTEIN PHOSPHORYLATION; PROTEOMICS; ALGORITHM; ANIMAL; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; ENZYME SPECIFICITY; HIGH THROUGHPUT SCREENING; HUMAN; METABOLISM; PHOSPHORYLATION; PROCEDURES; PROTEIN DATABASE; PROTEIN PROCESSING; WORKFLOW;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; PHOSPHOPROTEINS; PHOSPHORYLATION; PROTEIN KINASES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; SOFTWARE; SUBSTRATE SPECIFICITY; WORKFLOW;

EID: 84947968063     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3049-4_21     Document Type: Chapter

References (17)

1. Olsen JV et al (2010) Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal 3(104):ra3
2. Sharma K et al (2014) Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Rep 8(5):1583–1594
3. Manning G et al (2002) The protein kinase complement of the human genome. Science 298(5600):1912–1934
4. Dinkel H et al (2011) Phospho.ELM a database of phosphorylation sites--update 2011. Nucleic Acids Res 39(Database issue):D261–D267
5. Rask-Andersen M et al (2014) Advances in kinase targeting: current clinical use and clinical trials. Trends Pharmacol Sci 35(11): 604–620
6. Hornbeck PV et al (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res 40(Database issue):D261–D270
7. Gnad F, Gunawardena J, Mann M (2011) PHOSIDA 2011: the posttranslational modifi- cation database. Nucleic Acids Res 39(Database issue):D253–D260
8. Gnad F et al (2007) PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Genome Biol 8(11):R250
9. Olsen JV et al (2006) Global, in vivo, and sitespecific phosphorylation dynamics in signaling networks. Cell 127(3):635–648
10. Miller ML et al (2008) Linear motif atlas for phosphorylation-dependent signaling. Sci Signal 1(35):2
11. Yaffe MB et al (2001) A motif-based profile scanning approach for genome-wide prediction of signaling pathways. Nat Biotechnol 19(4): 348–353
12. Obenauer JC, Cantley LC, Yaffe MB (2003) Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res 31(13):3635–3641
13. Songyang Z et al (1994) Use of an oriented peptide library to determine the optimalsubstrates of protein kinases. Curr Biol 4(11): 973–982
14. Horn H et al (2014) KinomeXplorer: an integrated platform for kinome biology studies. Nat Methods 11(6):603–604
15. Linding R et al (2007) Systematic discovery of in vivo phosphorylation networks. Cell 129(7):1415–1426
16. Franceschini A et al (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 41(Database issue):D808–D815
17. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteomewide protein quantification. Nat Biotechnol 26(12):1367–1372