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PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites
Florian Gnad, Shubin Ren, Juergen Cox, Jesper V Olsen, Boris Macek, Mario Oroshi, Matthias Mann
Genome Biol. 2007; 8(11): R250. Published online 2007 November 26. doi: 10.1186/gb-2007-8-11-r250
PMCID:
PMC2258193
Abstract Full Text PDF–2.0M Supplementary Material
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 Is Cited by the Following 74 Articles in this Archive:
A Dynamic View of Domain-Motif Interactions
Eyal Akiva, Gilgi Friedlander, Zohar Itzhaki, Hanah Margalit
PLoS Comput Biol. 2012 January; 8(1): e1002341. Published online 2012 January 12. doi: 10.1371/journal.pcbi.1002341
Correction in:
PLoS Comput Biol. 2012 January; 8(1): 10.1371/annotation/2e21b1b9-46de-4cbe-a2a4-b4598d90d492.
PMCID:
PMC3257277
Abstract Full Text PDF–532K Supplementary Material Correction
Prediction of Protein Modification Sites of Pyrrolidone Carboxylic Acid Using mRMR Feature Selection and Analysis
Lu-Lu Zheng, Shen Niu, Pei Hao, KaiYan Feng, Yu-Dong Cai, Yixue Li
PLoS One. 2011; 6(12): e28221. Published online 2011 December 9. doi: 10.1371/journal.pone.0028221
PMCID:
PMC3235115
Abstract Full Text PDF–411K Supplementary Material
Profiling the Trypanosoma cruzi Phosphoproteome
Fabricio K. Marchini, Lyris M. F. de Godoy, Rita C. P. Rampazzo, Daniela P. Pavoni, Christian M. Probst, Florian Gnad, Matthias Mann, Marco A. Krieger
PLoS One. 2011; 6(9): e25381. Published online 2011 September 22. doi: 10.1371/journal.pone.0025381
PMCID:
PMC3178638
Abstract Full Text PDF–402K Supplementary Material
Unbiased Functional Proteomics Strategy for Protein Kinase Inhibitor Validation and Identification of bona fide Protein Kinase Substrates: Application to Identification of EEF1D as a Substrate for CK2
Laszlo Gyenis, James S. Duncan, Jacob P. Turowec, Maria Bretner, David W. Litchfield
J Proteome Res. 2011 November 4; 10(11): 4887–4901. Published online 2011 September 21. doi: 10.1021/pr2008994
PMCID:
PMC3208357
Abstract Full Text PDF–3.0M Supplementary Material
Unbiased Functional Proteomics Strategy for Protein Kinase Inhibitor Validation and Identification of bona fide Protein Kinase Substrates: Application to Identification of EEF1D as a Substrate for CK2
Laszlo Gyenis, James S. Duncan, Jacob P. Turowec, Maria Bretner, David W. Litchfield
J Proteome Res. 2011 November 4; 10(11): 4887–4901. Published online 2011 September 21. doi: 10.1021/pr2008994
PMCID:
PMC3208357
Abstract Full Text PDF–3.0M Supplementary Material
Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database
George A. Khoury, Richard C. Baliban, Christodoulos A. Floudas
Sci Rep. 2011; 1: 90. Published online 2011 September 13. doi: 10.1038/srep00090
PMCID:
PMC3201773
Abstract Full Text PDF–1.4M Supplementary Material
CDK5 Is Essential for Soluble Amyloid β-Induced Degradation of GKAP and Remodeling of the Synaptic Actin Cytoskeleton
Francesco Roselli, Paolo Livrea, Osborne F. X. Almeida
PLoS One. 2011; 6(7): e23097. Published online 2011 July 29. doi: 10.1371/journal.pone.0023097
PMCID:
PMC3146526
Abstract Full Text PDF–4.9M Supplementary Material
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs
Frank Wessely, Martin Bartl, Reinhard Guthke, Pu Li, Stefan Schuster, Christoph Kaleta
Mol Syst Biol. 2011; 7: 515. Published online 2011 July 19. doi: 10.1038/msb.2011.46
PMCID:
PMC3159982
Abstract Full Text PDF–565K Supplementary Material
PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity
Tzong-Yi Lee, Neil Arvin Bretaña, Cheng-Tsung Lu
BMC Bioinformatics. 2011; 12: 261. Published online 2011 June 26. doi: 10.1186/1471-2105-12-261
PMCID:
PMC3228547
Abstract Full Text PDF–1.8M Supplementary Material
Mining the TRAF6/p62 interactome for a selective ubiquitination motif
Trafina S Jadhav, Marie W Wooten, Michael C Wooten
BMC Proc. 2011; 5(Suppl 2): S4. Published online 2011 May 28. doi: 10.1186/1753-6561-5-S2-S4
PMCID:
PMC3090762
Abstract Full Text PDF–1.2M
Discovery of Protein Phosphorylation Motifs through Exploratory Data Analysis
Yi-Cheng Chen, Kripamoy Aguan, Chu-Wen Yang, Yao-Tsung Wang, Nikhil R. Pal, I-Fang Chung
PLoS One. 2011; 6(5): e20025. Published online 2011 May 25. doi: 10.1371/journal.pone.0020025
PMCID:
PMC3102080
Abstract Full Text PDF–588K Supplementary Material
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes
Viswanadham Sridhara, Aron Marchler-Bauer, Stephen H. Bryant, Lewis Y. Geer
Database (Oxford) 2011; 2011: bar019. Published online 2011 May 13. doi: 10.1093/database/bar019
PMCID:
PMC3096321
Abstract Full Text PDF–554K
Evolutionary patterns of phosphorylated serines
Yerbol Z Kurmangaliyev, Alexander Goland, Mikhail S Gelfand
Biol Direct. 2011; 6: 8. Published online 2011 February 9. doi: 10.1186/1745-6150-6-8
PMCID:
PMC3044110
Abstract Full Text PDF–499K
Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map
Nozomu Yachie, Rintaro Saito, Naoyuki Sugiyama, Masaru Tomita, Yasushi Ishihama
PLoS Comput Biol. 2011 January; 7(1): e1001064. Published online 2011 January 27. doi: 10.1371/journal.pcbi.1001064
PMCID:
PMC3029238
Abstract Full Text PDF–512K Supplementary Material
Deciphering Human Heat Shock Transcription Factor 1 Regulation via Post-Translational Modification in Yeast
Liliana Batista-Nascimento, Daniel W. Neef, Phillip C. C. Liu, Claudina Rodrigues-Pousada, Dennis J. Thiele
PLoS One. 2011; 6(1): e15976. Published online 2011 January 6. doi: 10.1371/journal.pone.0015976
PMCID:
PMC3017095
Abstract Full Text PDF–892K
Mining recent brain proteomic databases for ion channel phosphosite nuggets
Oscar Cerda, Je-Hyun Baek, James S. Trimmer
J Gen Physiol. 2011 January; 137(1): 3–16. doi: 10.1085/jgp.201010555
PMCID:
PMC3010060
Abstract Full Text PDF–1.2M
The Musite open-source framework for phosphorylation-site prediction
Jianjiong Gao, Dong Xu
BMC Bioinformatics. 2010; 11(Suppl 12): S9. Published online 2010 December 21. doi: 10.1186/1471-2105-11-S12-S9
PMCID:
PMC3040535
Abstract Full Text PDF–752K
Mass Spectrometric Analysis of Lysine Ubiquitylation Reveals Promiscuity at Site Level
Jannie M. R. Danielsen, Kathrine B. Sylvestersen, Simon Bekker-Jensen, Damian Szklarczyk, Jon W. Poulsen, Heiko Horn, Lars J. Jensen, Niels Mailand, Michael L. Nielsen
Mol Cell Proteomics. 2011 March; 10(3): M110.003590. Published online 2010 December 7. doi: 10.1074/mcp.M110.003590
PMCID:
PMC3047152
Abstract Full Text
Mass spectrometry mapping of epidermal growth factor receptor phosphorylation related to oncogenic mutations and tyrosine kinase inhibitor sensitivity
Guolin Zhang, Bin Fang, Richard Z. Liu, Huiyi Lin, Fumi Kinose, Yun Bai, Umut Oguz, Elizabeth R. Remily-Wood, Jiannong Li, Soner Altiok, Steven Eschrich, John Koomen, Eric B. Haura
J Proteome Res. Author manuscript; available in PMC 2012 January 7.
Published in final edited form as: J Proteome Res. 2011 January 7; 10(1): 305–319. Published online 2010 December 3. doi: 10.1021/pr1006203
PMCID:
PMC3050523
Abstract Full Text PDF–2.8M Supplementary Material
PHOSIDA 2011: the posttranslational modification database
Florian Gnad, Jeremy Gunawardena, Matthias Mann
Nucleic Acids Res. 2011 January; 39(Database issue): D253–D260. Published online 2010 November 16. doi: 10.1093/nar/gkq1159
PMCID:
PMC3013726
Abstract Full Text PDF–9.8M
Identifying Human Kinase-Specific Protein Phosphorylation Sites by Integrating Heterogeneous Information from Various Sources
Tingting Li, Pufeng Du, Nanfang Xu
PLoS One. 2010; 5(11): e15411. Published online 2010 November 15. doi: 10.1371/journal.pone.0015411
PMCID:
PMC2981550
Abstract Full Text PDF–273K Supplementary Material
Uncovering new substrates for Aurora A kinase
Teresa Sardon, Roland A Pache, Amelie Stein, Henrik Molina, Isabelle Vernos, Patrick Aloy
EMBO Rep. 2010 December; 11(12): 977–984. Published online 2010 November 12. doi: 10.1038/embor.2010.171
PMCID:
PMC2999863
Abstract Full Text PDF–966K Supplementary Material
Phospho.ELM: a database of phosphorylation sites—update 2011
Holger Dinkel, Claudia Chica, Allegra Via, Cathryn M. Gould, Lars J. Jensen, Toby J. Gibson, Francesca Diella
Nucleic Acids Res. 2011 January; 39(Database issue): D261–D267. Published online 2010 November 8. doi: 10.1093/nar/gkq1104
PMCID:
PMC3013696
Abstract Full Text PDF–3.8M
Confident Phosphorylation Site Localization Using the Mascot Delta Score
Mikhail M. Savitski, Simone Lemeer, Markus Boesche, Manja Lang, Toby Mathieson, Marcus Bantscheff, Bernhard Kuster
Mol Cell Proteomics. 2011 February; 10(2): M110.003830. Published online 2010 November 6. doi: 10.1074/mcp.M110.003830
PMCID:
PMC3033680
Abstract Full Text
Toward a complete in silico, multi-layered embryonic stem cell regulatory network
Huilei Xu, Christoph Schaniel, Ihor R. Lemischka, Avi Ma’ayan
Wiley Interdiscip Rev Syst Biol Med. Author manuscript; available in PMC 2010 November 1.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2010 Nov–Dec; 2(6): 708–733. doi: 10.1002/wsbm.93
PMCID:
PMC2951283
Abstract Full Text PDF–1.9M
RegPhos: a system to explore the protein kinase–substrate phosphorylation network in humans
Tzong-Yi Lee, Justin Bo-Kai Hsu, Wen-Chi Chang, Hsien-Da Huang
Nucleic Acids Res. 2011 January; 39(Database issue): D777–D787. Published online 2010 October 30. doi: 10.1093/nar/gkq970
PMCID:
PMC3013804
Abstract Full Text PDF–7.8M
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites
Andreas Zanzoni, Daniel Carbajo, Francesca Diella, Pier Federico Gherardini, Anna Tramontano, Manuela Helmer-Citterich, Allegra Via
Nucleic Acids Res. 2011 January; 39(Database issue): D268–D271. Published online 2010 October 21. doi: 10.1093/nar/gkq936
PMCID:
PMC3013787
Abstract Full Text PDF–2.4M
Rapid and transient recruitment of DNMT1 to DNA double-strand breaks is mediated by its interaction with multiple components of the DNA damage response machinery
Kyungsoo Ha, Gun Eui Lee, Stela S. Palii, Kevin D. Brown, Yoshihiko Takeda, Kebin Liu, Kapil N. Bhalla, Keith D. Robertson
Hum Mol Genet. 2011 January 1; 20(1): 126–140. Published online 2010 October 11. doi: 10.1093/hmg/ddq451
PMCID:
PMC3000680
Abstract Full Text PDF–733K Supplementary Material
Integrated data management and validation platform for phosphorylated tandem mass spectrometry data
Anna-Maria Lahesmaa-Korpinen, Scott M. Carlson, Forest M. White, Sampsa Hautaniemi
Proteomics. Author manuscript; available in PMC 2011 October 1.
Published in final edited form as: Proteomics. 2010 October; 10(19): 3515–3524. doi: 10.1002/pmic.200900727
PMCID:
PMC3017393
Abstract Full Text PDF–1002K Supplementary Material
A Strategy for Interaction Site Prediction between Phospho-binding Modules and their Partners Identified from Proteomic Data
Willy Aucher, Emmanuelle Becker, Emilie Ma, Simona Miron, Arnaud Martel, Françoise Ochsenbein, Marie-Claude Marsolier-Kergoat, Raphaël Guerois
Mol Cell Proteomics. 2010 December; 9(12): 2745–2759. Published online 2010 September 10. doi: 10.1074/mcp.M110.003319
PMCID:
PMC3101860
Abstract Full Text Supplementary Material
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