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Links tagged with 'phosphorylation'

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CRPDatabase Content

http://fasta.bioch.virginia.edu/crp/

Protein > Domains and Motifs
Protein > Sequence Features

Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.

NAR Web Server Issue 2003
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tagsamino acid sequence biochemistry dna sequence analysis humans molecular sequence data neoplasm proteins neural networks (computer) phosphoproteins phosphorylation phosphoserine phosphothreonine phosphotyrosine protein sequence analysis proteins radioactive tracers recombinant proteins sensitivity and specificity

GPSTool Content

http://csbl.bmb.uga.edu/~ffzhou/gps_web/

Protein > Domains and Motifs

Using datasets of known phosphorylation sites, the Group based Phosphorylation Scoring method (GPS) allows the prediction of kinase specific phosphorylation sites from primary protein sequences.

This content is being maintained by ffzhou.

NAR Web Server Issue 2005
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tagsalgorithms amino acid sequence homology animals binding sites conserved sequence microfilament proteins nerve tissue proteins phosphoproteins phosphorylation protein binding protein kinases protein sequence analysis protein-serine-threonine kinases rats sequence alignment substrate specificity

KinasePhosTool Content

http://kinasephos.mbc.nctu.edu.tw/

Protein > Domains and Motifs

KinasePhos is a tool for identifying kinase-specific phosphorylation sites in protein sequences.

NAR Web Server Issue 2005
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tagscomputational biology markov chains phosphoproteins phosphorylation protein kinases protein sequence analysis

KinasePhos 2.0Tool Content

http://kinasephos2.mbc.nctu.edu.tw/

Protein > Domains and Motifs

KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.

NAR Web Server Issue 2007
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tagscatalytic domain computational biology computer simulation markov chains neural networks (computer) phosphoproteins phosphorylation probability protein kinases protein sequence analysis sensitivity and specificity

NetPhosTool Content

http://www.cbs.dtu.dk/services/NetPhos/

Protein > Sequence Features

NetPhos is a neural network-based method for predicting potential phosphorylation sites at serine, threonine or tyrosine residues in protein sequences

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tagsamino acid motifs amino acid sequence animals binding sites consensus sequence eukaryotic cells glycosylation molecular models neural networks (computer) nuclear proteins phosphoproteins phosphorylation phylogeny reproducibility of results sensitivity and specificity serine substrate specificity tertiary protein structure threonine trans-activators tyrosine

PhosPhAtDatabase Content

http://phosphat.mpimp-golm.mpg.de/

Model Organisms > Databases

The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 3.0) contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide properties, their annotated biological function as well as the experimental and analytical context is given. For a majority of peptides, the actual annotated mass spectrum is displayed in interactive manner.

This content is being maintained by Waltraud Schulze.

NAR Database Issue 2010
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tagsarabidopsis arabidopsis proteins binding sites computational biology genetic databases mass spectrometry phosphopeptides phosphoproteins phosphorylation phosphoserine plant genes plant genome protein databases protein sequence analysis

Phospho.ELMDatabase Content

http://phospho.elm.eu.org/

Protein > Domains and Motifs

Database of experimentally verified phosphorylation sites in eukaryotic proteins. Annotations are done manually and database entries come from and are linked back to scientific literature. Phospho.ELM incorporates the data formerly found in PhosphoBase.

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tagsanimals binding sites humans mice phosphorylation post-translational protein processing protein databases proteins rats research design

Phospho.ELMDatabase Content

http://phospho.elm.eu.org

Protein > Databases

The Phospho.ELM resource is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource comprises serine, threonine and tyrosine non-redundant phosphorylation sites. New features include: structural disorder/order and accessibility information and a conservation score. Additionally, the conservation of the phosphosites can be visualized directly on the multiple sequence alignment used for the score calculation.

NAR Database Issue 2011
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tagsamino acid sequence animals conserved sequence humans mice phosphoproteins phosphorylation protein conformation protein databases protein sequence analysis serine threonine tyrosine

Phospho3D 2.0Database Content

http://www.phospho3d.org/

Protein > Databases

Phospho3D is a database of 3D structures of phosphorylation sites derived from Phospho.ELM. The database provides the results of a large-scale structural comparison of the 3D zones versus a representative dataset of structures, thus associating to each P-site a number of structurally similar sites. Phopsho3D has now many new features. Moreover, it features P3Dscan, a new functionality that allows the user to submit a protein structure and scan it against the 3D zones collected in Phospho3D.

This content is being maintained by azanzoni.

NAR Database Issue 2011
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external linksLink on Twitter
tagsphosphoproteins phosphorylation protein conformation protein databases

PhosphoSiteDatabase Content

http://www.phosphosite.org/

Protein > Domains and Motifs

PhosphoSite is a curated database of in vivo human and mouse phosphorylation sites. The database contains peptide sequences and locations within domains and motifs for the phosphorylation sites, and links to useful resources and literature references. For educational users, information extracted from the public domain is freely available.

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tagsanimals computational biology cultured cells factual databases humans mice phosphorylation proteins

PredikinTool Content

http://predikin.biosci.uq.edu.au

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation

NAR Web Server Issue 2008
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tagsamino acid sequence animals binding sites catalytic domain mice peptides phosphorylation protein databases protein kinases protein sequence analysis protein-serine-threonine kinases substrate specificity

RegPhosDatabase Content

http://RegPhos.mbc.nctu.edu.tw

Protein > Databases

RegPhos is a database for exploration of the phosphorylation network associated with an input of genes/proteins. Subcellular localization information is also included.

NAR Database Issue 2011
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tagsgene expression profiling humans insulin receptor substrate proteins phosphoproteins phosphorylation protein databases protein interaction mapping protein kinases signal transduction

ScansiteTool Content

http://scansite.mit.edu/

Protein > Domains and Motifs

Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.

NAR Web Server Issue 2003
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tagsalgorithms amino acid motifs amino acid sequence animals binding sites cattle cdc2 protein kinase cdc2-cdc28 kinases computational biology consensus sequence cyclic amp-dependent protein kinases cyclin-dependent kinase 2 cyclin-dependent kinases factual databases fungal proteins genome humans mice mitogen-activated protein kinase kinases molecular models molecular sequence data molecular structure peptides phosphorylation protein binding protein conformation protein databases protein interaction mapping protein kinases protein sequence analysis protein-serine-threonine kinases proteins proteome rats saccharomyces cerevisiae proteins serine signal transduction substrate specificity tertiary protein structure threonine tyrosine