NetPhorest 2.1 – Model Phosphorylation driven Cellular Signaling Networks

NetPhorest 2.1

:: DESCRIPTION

NetPhorest integrates in vitro kinase and phosphopeptide-binding domain specificity assays with publically accessible known in vivo substrate lists in order to generate substrate specificity descriptions for individual proteins as well as protein families.

::DEVELOPER

NetPhorest team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 NetPhorest

:: MORE INFORMATION

Citation

Miller et al.,
Linear Motif Atlas for Phosphorylation-Dependent Signaling.
Science Signaling, 2 September 2008, Vol 1, Issue 35, p. ra2.

Motif-All 1.0 – Discovering All Phosphorylation Motifs

Motif-All 1.0

:: DESCRIPTION

The Motif-All algorithm discovers motifs from a set of phosphorylated sequences P and a much larger set of background sequences N.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

Motif-All

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

  Motif-All

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S22. doi: 10.1186/1471-2105-12-S1-S22.
Motif-All: discovering all phosphorylation motifs.
He Z1, Yang C, Guo G, Li N, Yu W.

PhosNetConstruct – Phosphorylation Network Reconstruction

PhosNetConstruct

:: DESCRIPTION

PhosNetConstruct is a tool to predict novel phosphorylation networks based on the preference of certain kinase families to phosphorylate specific functional protein families (domains). It identifies the potentially phosphorylated proteins from a given set of proteins and predicts target kinases which in turn would phosphorylate these identified phosphoproteins based on their domain compositions.

::DEVELOPER

PhosNetConstruct team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):1730-8. doi: 10.1093/bioinformatics/btu112. Epub 2014 Feb 25.
Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network.
Damle NP, Mohanty D.

MIMP – Predicting the Impact of Mutations on Kinase-substrate Phosphorylation

MIMP

:: DESCRIPTION

MIMP characterizes genetic variants such as cancer mutations that specifically alter kinase-binding sites in proteins.

::DEVELOPER

Bader Lab University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser / Linux
  • R

:: DOWNLOAD

MIMP

:: MORE INFORMATION

Citation

MIMP: predicting the impact of mutations on kinase-substrate phosphorylation.
Wagih O, Reimand J, Bader GD.
Nat Methods. 2015 Jun;12(6):531-3. doi: 10.1038/nmeth.3396.

DAPPLE 2 – Homology-based Prediction of Phosphorylation Sites

DAPPLE 2

:: DESCRIPTION

DAPPLE is a homology-based method for predicting phosphorylation sites in an organism of interest. It uses BLAST searches of experimentally-determined phosphorylation sites in one organism (or several organisms) to predict phosphorylation sites in an organism of interest. It outputs a table containing information helpful for choosing phosphorylation sites that are of interest to you, such as the number of sequence differences between the query site and the hit site, the location of the query site and the hit site in their respective intact proteins, and whether the corresponding intact proteins are reciprocal BLAST hits (and thus predicted orthologues).

::DEVELOPER

Bioinformatics Research Group, University of Saskatchewan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

DAPPLE 2: a tool for the homology-based prediction of post-translational modification sites.
Trost B, Maleki F, Kusalik A, Napper S.
J Proteome Res. 2016 Jul 1.

Bioinformatics. 2013 Jul 1;29(13):1693-5. doi: 10.1093/bioinformatics/btt265. Epub 2013 May 8.
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites.
Trost B, Arsenault R, Griebel P, Napper S, Kusalik A.

HMMpTM – Transmembrane Protein Topology Prediction using Phosphorylation and Glycosylation Site Prediction

HMMpTM

:: DESCRIPTION

HMMpTM is a Hidden Markov Model based method capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites across the protein sequence.

::DEVELOPER

The Biophysics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Biochim Biophys Acta. 2014 Feb;1844(2):316-22. doi: 10.1016/j.bbapap.2013.11.001. Epub 2013 Nov 10.
HMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction.
Tsaousis GN, Bagos PG, Hamodrakas SJ.

PlantPhos – Plant Phosphorylation Prediction Tool

PlantPhos

:: DESCRIPTION

PlantPhos is a web tool for predicting potential phosphorylation sites in plant proteins.

::DEVELOPER

CSB Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity.
Lee TY, Bretaña NA, Lu CT.
BMC Bioinformatics. 2011 Jun 26;12:261. doi: 10.1186/1471-2105-12-261.

SubPhosPred – Prediction of Phosphorylation Sites

SubPhosPred

:: DESCRIPTION

SubPhosPred is a web server that could predict phosphosrylation sites in different subcellular compartments (SCs) of homo sapiens, which combines a novel discrete wavelet transform (DWT) strategy with support vector machine (SVM) approach to identify phosphorylation sites for different SCs in human.

::DEVELOPER

the Qiu Lab. NanChang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Xiang Chen, Shao-Ping Shi, Sheng-Bao Suo, Hao-Dong Xu, Jian-Ding Qiu*.
Proteomic Analysis and Prediction of Human Phosphorylation Sites in Subcellular Level Reveals Subcellular Specificity,
Bioinformatics, 2015, 31,194-200.

PPTM 1.0 – Literature Mining of Protein Phosphorylation Using Dependency Parse Trees

PPTM 1.0

:: DESCRIPTION

PPTM is a web tool of novel text-mining method for efficiently retrieving and extracting protein phosphorylation information from literature.

::DEVELOPER

HI_Lab @ USTC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Literature mining of protein phosphorylation using dependency parse trees.
Wang M, Xia H, Sun D, Chen Z, Wang M, Li A.
Methods. 2014 Jun 1;67(3):386-93. doi: 10.1016/j.ymeth.2014.01.008.

PhosphoPICK – Phosphorylation in a Protein Interaction Context for Kinases

PhosphoPICK

:: DESCRIPTION

PhosphoPICK is a method for predicting kinase substrates using cellular context information, and is currently able to make predictions for 59 human kinases.

::DEVELOPER

Boden lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PhosphoPICK: Modelling Cellular Context to Map Kinase-Substrate Phosphorylation Events.
Patrick R, Lê Cao KA, Kobe B, Bodén M.
Bioinformatics. 2014 Oct 9. pii: btu663