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CPhos specifications

Information


Unique identifier OMICS_20954
Name CPhos
Software type Application/Script
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Fahad Saeed

Information


Unique identifier OMICS_20954
Name CPhos
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Input data Phosphopeptides and species.
Output data A summary page, list of phosphopeptides, phosphosites, phosphoproteins, orthologs, sequence alignments, and conservation scores.
Output format CSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Fahad Saeed

Publication for CPhos

CPhos citations

 (7)
library_books

Phosphorylation of residues inside the SNARE complex suppresses secretory vesicle fusion

2016
PMCID: 5010044
PMID: 27402227
DOI: 10.15252/embj.201694071

[…] To assess the conservation of phosphorylation sites among different species, we used the standalone versions of CPhos (Zhao et al, ) (http://helixweb.nih.gov/CPhos) to calculate a score for each identified phosphorylation site in our phosphoproteomics data. Only phosphorylation sites with a perfect phosphorylat […]

library_books

Computational Analysis of the Predicted Evolutionary Conservation of Human Phosphorylation Sites

2016
PLoS One
PMCID: 4821552
PMID: 27046079
DOI: 10.1371/journal.pone.0152809

[…] sites with a database of experimentally-determined phosphorylation sites and a phosphorylation site prediction algorithm. Another software program devoted to the evolution of phosphorylation sites is CPhos, which—based on the assumption that functional phosphorylation sites are more likely to be conserved than non-functional sites—aids the user in identifying functional phosphorylation sites by as […]

library_books

A Systems Level Analysis of Vasopressin mediated Signaling Networks in Kidney Distal Convoluted Tubule Cells

2015
Sci Rep
PMCID: 4523861
PMID: 26239621
DOI: 10.1038/srep12829

[…] 733 are unique to this study (). 5191 of the identified phosphorylation sites had a phosphoRS score above 80. To determine the potential functional significances of the phosphorylation sites, we used CPhos. The majority of sites had a site conservation score greater than 0.9 (Supplemental ) indicating that they were highly conserved sites between species and evolution and suggesting that they have […]

library_books

Original 2 (3 Alkoxy 1H pyrazol 1 yl)azines Inhibitors of Human Dihydroorotate Dehydrogenase (DHODH)

2015
J Med Chem
PMCID: 4516315
PMID: 26079043
DOI: 10.1021/acs.jmedchem.5b00606

[…] by the titration method previously reported. Second step: Compound 12c (0.31 g, 0.96 mmol), palladium acetate (0.011 g, 0.048 mmol), and 2-dicyclohexylphosphino-2′,6′-bis(N,N-dimethylamino)biphenyl (CPhos) (0.042 g, 0.096 mmol) were added in a flask flushed with argon. The decanted solution of (1-phenylethyl)zinc chloride described above (6.1 mL, 2.89 mmol) was injected, and the mixture heated fo […]

library_books

Rational Ligand Design for the Arylation of Hindered Primary Amines Guided by Reaction Progress Kinetic Analysis

2015
J Am Chem Soc
PMCID: 4379963
PMID: 25651374
DOI: 10.1021/ja512903g

[…] triisopropyl substituents with two dimethylamino groups (L4) also gave the desired product in good yield (Table , entry 4). The catalyst derived from the corresponding dicyclohexylphosphino analogue, CPhos (L5), gave no product, suggesting that the relatively smaller and less electron-donating phenyl groups on the phosphine atom are required to promote the desired transformation.The most effective […]

library_books

Global Analysis of Neuronal Phosphoproteome Regulation by Chondroitin Sulfate Proteoglycans

2013
PLoS One
PMCID: 3601063
PMID: 23527152
DOI: 10.1371/journal.pone.0059285

[…] levance of a discovered phosphosite is to assess the evolutionary conservation of these sites across species since functionally relevant sites would be expected to be highly conserved . We hence used CPhos , a program developed in our institute (available at: http://helixweb.nih.gov/CPhos/) to identify evolutionarily conserved functional phosphorylation sites . We then evaluated the conserved site […]


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CPhos institution(s)
National Heart, Lung, and Blood Institute (NHLBI), Epithelial Systems Biology Laboratory, National Institutes of Health (NIH), Bethesda, MD, USA
CPhos funding source(s)
Supported by the Intramural Budget of the NHLBI (NHLBI Project no. Z01-HL- 001285).

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