Post-translational modifications prediction methods
A list of Bioinformatic tools usefull for Post-translational modifications prediction methods :
Human Protein Reference Database (HPRD) : a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
UNIMOD : protein modifications for mass spectrometry.
Phosphorylation :
Ascore : a probability-based score which measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra.
http://ascore.med.harvard.edu/
GPS : computational prediction of phosphorylation sites with their cognate protein kinases.
KinasePhos 2.0 : kinase-specific phosphorylation site prediction tool.
http://kinasephos2.mbc.nctu.edu.tw/
Motif-x : a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.
http://motif-x.med.harvard.edu/
MetaPredPS : meta-predicting strategies for the serine/threonine phosphorylation site prediction.
http://metapred.biolead.org/MetaPredPS/
NetPhos 2.0 : a neural network-based method for the prediction of potential phosphorylation sites.
http://www.cbs.dtu.dk/services/NetPhos/
NetPhosK 1.0 : used to predict kinase specific phosphorylation sites.
http://www.cbs.dtu.dk/services/NetPhosK/
NetPhoRest : a non-redundant collection of 125 sequence-based classifiers for linear motifs in phosphorylation-dependent signaling.
NetworKIN : a method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins.
http://networkin.info/search.php
Phosida : allows the retrieval of phosphorylation, acetylation, and N-glycosylation data of any protein of interest.
Phospho.ELM database : contains a collection of experimentally verified Ser, Thr and Tyr sites in eukaryotic proteins.
Phosphomotif Finder : reports the PRESENCE of any literature-derived motif in the query sequence.
http://www.hprd.org/PhosphoMotif_finder
PhosphoPep : provide interactive interrogation of MS-derived phosphorylation data from 4 different organisms.
PhosphoScore : a phosphorylation assignment program that is compatible with all levels of tandem mass spectrometry spectra (MSn) generated through the Bioworks/Sequest platform.
http://dir.nhlbi.nih.gov/papers/lkem/phosphoscore/
PhosphoSitePlus : tools for the study of protein post-translational modifications (PTMs). Provide an extensive, manually curated phosphorylation site database.
pkaPS : Prediction of protein kinase A phosphorylation sites using the simplified kinase binding model.
http://mendel.imp.ac.at/pkaPS/
PPSP : Prediction of PK-Specific Phosphorylation Site.
Predikin : Predikin is a system to predict substrate specificity of protein kinases.
http://predikin.biosci.uq.edu.au/
ScanSite : scan for protein motif
SLoMo : a tool which enables researchers to localise sites of post-translational modifications to peptides identified in mass spectrometry experiments.
http://massspec.bham.ac.uk/slomo
Acetylation :
Phosida : allows the retrieval of phosphorylation, acetylation, and N-glycosylation data of any protein of interest
PhosphoSitePlus : tools for the study of protein post-translational modifications (PTMs).
Methylation :
PhosphoSitePlus : tools for the study of protein post-translational modifications (PTMs).
N-Glycosylation :
Phosida : allows the retrieval of phosphorylation, acetylation, and N-glycosylation data of any protein of interest
O-Glycosylation :
PhosphoSitePlus : tools for the study of protein post-translational modifications (PTMs).
YinOYang 1.2 : method capable of predicting potential O-ß-GlcNAc attachment sites in eukaryotic proteins. This method is also capable to predict potential phosphoryaltion sites and thus predict Yin Yang sites.
http://www.cbs.dtu.dk/services/YinOYang/
Sumoylation :
PhosphoSitePlus : tools for the study of protein post-translational modifications (PTMs).
Ubiquitination :
PhosphoSitePlus : tools for the study of protein post-translational modifications (PTMs).
Yin Yang sites :
= residues where O-ß-GlcNAc and phosphorylation compete for each other.
YinOYang 1.2 : method capable of predicting potential O-ß-GlcNAc attachment sites in eukaryotic proteins. This method is also capable to predict potential phosphoryaltion sites and thus predict Yin Yang sites.
http://www.cbs.dtu.dk/services/YinOYang/
Post-translational modifications prediction methods – PTM prediction methods – PTM prediction – Post-translational modifications – PTM – prediction methods
Post-translational modifications prediction methods – PTM prediction methods – PTM prediction – Post-translational modifications prediction method
