Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources

Table 7 Visualization, data retrieval, and prediction tools

Tool	Last update	Version	Type	Input	Output	Method of access	References
CPhos	2012	1.3	Phosphorylation site conservation	Phosphopeptides	Conservation scores	Tool	[101]
PhosphoLogo	2012		Visualization of sequence motifs	Sequence motifs	Motif visualization	Tool	[98]
RegPhos2.0	2013	2.0	Visualization of kinase data	Gene names	Network visualization or cancer gene expression	Web\|DL	[42, 113]
eFIP	2014		Returns publications involving phosphorylation	Gene names or words	Publications matching those words	Web	[100]
RLIMS-P	2014	2.0	returns protein phosphorylation information from literature	PMIDs or keywords	kinase, substrate, and site	Web\|DL	[99]
PyTMs	2015	1.2	pyMOL plugin to add PTMs to protein models	Protein models, PTMs	PTMs integrated in protein models	Tool	[102]
14-3-3-Pred	2015		Predicts 14-3-3 binding phosphosite	Protein sequences	Predicted 14-3-3 binding sites	Web\|DL	[103]
KinMap	2016		Kinome tree visualization	Kinases	Tree with highlighted branches	Web\|DL	[97]
KinConform	2017		Determines which structures are kinases	Structures	Active or inactive kinase chains	Tool	[96]
Kinannote	2017	1.0	Classifies sequences as kinases	Protein sequences	Kinase annotation	Tool	[95]

ISSN: 1559-0275