Difference between revisions of "Phosphatome Computational Tools and Resources"
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| + | __NOTOC__ | ||
| + | [[Technical Notes]]: [[Phosphatome_Computational_Tools_and_Resources]] | ||
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===== PTP.cshl ===== | ===== PTP.cshl ===== | ||
[http://ptp.cshl.edu/ PTP.cshl] focuses on protein tyrosine phosphatases. It was launched in 2011 and provided a most complete census on human protein tyrosine phosphatases <cite>andersen-2001</cite>. However, the content of the web site seems not updated since 2005. | [http://ptp.cshl.edu/ PTP.cshl] focuses on protein tyrosine phosphatases. It was launched in 2011 and provided a most complete census on human protein tyrosine phosphatases <cite>andersen-2001</cite>. However, the content of the web site seems not updated since 2005. | ||
| + | |||
| + | ===== PhosphaBase ===== | ||
| + | [http://www.bioinf.manchester.ac.uk/phosphabase/index.html PhosphaBase] (PhB) is a database of protein phosphatases and contains information about their protein sequences <cite>phosphabase04</cite>. It is not updated any more, though. | ||
| + | |||
| + | ===== DEPOD ===== | ||
| + | DEPOD is the human DEPhOsphorylation Database is a manually curated database collecting human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved. [http://www.koehnlab.de/depod/index.php Link] | ||
| + | |||
| + | ===== HuPho ===== | ||
| + | HuPho is an on-line web resource developed by the Molecular Genetics Group at the Department of Biology of the University of Rome Tor Vergata, to assist scientists in the task of recovering information about human phosphatases. The web site is designed to retrieve information about 245 proteins either containing a phosphatase domain or experimentally characterized as regulatory subunits. [http://hupho.uniroma2.it Link] | ||
===== PTP-central ===== | ===== PTP-central ===== | ||
| − | [http://www.ptp-central.org/ PTP-central] focuses on protein tyrosine phosphatases. It uses the same classification schema as the landmark work of Alonso et | + | [http://www.ptp-central.org/ PTP-central] focuses on protein tyrosine phosphatases. It uses the same classification schema as the landmark work of Alonso ''et al.'' <cite>alonso04</cite>. It comes with a tool (Y-Phosphatomer) to scan protein tyrosine phosphatases from genomes, and updated the total number of human protein tyrosine phosphatase to 109 <cite>ptp-central-2014</cite>. |
===== GeneNet™ Phosphatase shRNA Library ===== | ===== GeneNet™ Phosphatase shRNA Library ===== | ||
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#ptp-central-2014 pmid=23911837 | #ptp-central-2014 pmid=23911837 | ||
#andersen-2001 pmid=11585896 | #andersen-2001 pmid=11585896 | ||
| + | #alonso04 pmid=15186772 | ||
| + | #phosphabase04 pmid=15558746 | ||
</biblio> | </biblio> | ||
Latest revision as of 04:31, 10 April 2017
Technical Notes: Phosphatome_Computational_Tools_and_Resources
PTP.cshl
PTP.cshl focuses on protein tyrosine phosphatases. It was launched in 2011 and provided a most complete census on human protein tyrosine phosphatases [1]. However, the content of the web site seems not updated since 2005.
PhosphaBase
PhosphaBase (PhB) is a database of protein phosphatases and contains information about their protein sequences [2]. It is not updated any more, though.
DEPOD
DEPOD is the human DEPhOsphorylation Database is a manually curated database collecting human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved. Link
HuPho
HuPho is an on-line web resource developed by the Molecular Genetics Group at the Department of Biology of the University of Rome Tor Vergata, to assist scientists in the task of recovering information about human phosphatases. The web site is designed to retrieve information about 245 proteins either containing a phosphatase domain or experimentally characterized as regulatory subunits. Link
PTP-central
PTP-central focuses on protein tyrosine phosphatases. It uses the same classification schema as the landmark work of Alonso et al. [3]. It comes with a tool (Y-Phosphatomer) to scan protein tyrosine phosphatases from genomes, and updated the total number of human protein tyrosine phosphatase to 109 [4].
GeneNet™ Phosphatase shRNA Library
GeneNet™ Phosphatase shRNA Library provides a list of 244 phosphatases, but some genes on the list are probably not phosphatases, such as discs and speedy homolog A, SIRPA and etc.
References
- Andersen JN, Mortensen OH, Peters GH, Drake PG, Iversen LF, Olsen OH, Jansen PG, Andersen HS, Tonks NK, and Møller NP. Structural and evolutionary relationships among protein tyrosine phosphatase domains. Mol Cell Biol. 2001 Nov;21(21):7117-36. DOI:10.1128/MCB.21.21.7117-7136.2001 |
- Wolstencroft KJ, Stevens R, Tabernero L, and Brass A. PhosphaBase: an ontology-driven database resource for protein phosphatases. Proteins. 2005 Feb 1;58(2):290-4. DOI:10.1002/prot.20325 |
- Alonso A, Sasin J, Bottini N, Friedberg I, Friedberg I, Osterman A, Godzik A, Hunter T, Dixon J, and Mustelin T. Protein tyrosine phosphatases in the human genome. Cell. 2004 Jun 11;117(6):699-711. DOI:10.1016/j.cell.2004.05.018 |
- Hatzihristidis T, Liu S, Pryszcz L, Hutchins AP, Gabaldón T, Tremblay ML, and Miranda-Saavedra D. PTP-central: a comprehensive resource of protein tyrosine phosphatases in eukaryotic genomes. Methods. 2014 Jan 15;65(2):156-64. DOI:10.1016/j.ymeth.2013.07.031 |
