Tag: Phosphorylation

PHOSFER – PHOsphorylation Site FindER

PHOSFER

:: DESCRIPTION

PHOSFER uses a novel machine-learning approach in order to predict phosphorylation sites in soybean proteins, and will be expanded to predict for other plants in the future.

::DEVELOPER

Bioinformatics Research Group, University of Saskatchewan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

B. Trost and A. Kusalik.
Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights.
Bioinformatics 29(6):686-694, 2013.

PhosSNP 1.0 – Influence of Protein Phosphorylation by nsSNP

PhosSNP 1.0

:: DESCRIPTION

PhosSNP is a database of Phosphorylation-related SNP. we defined a phosphorylation-related SNP (phosSNP) as a non-synonymous SNP (nsSNP) that affects the protein phosphorylation status.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows / Linux / MacOsX
  • Java

:: DOWNLOAD

 PhosSNP

:: MORE INFORMATION

Citation

PhosSNP for Systematic Analysis of Genetic Polymorphisms That Influence Protein Phosphorylation
Jian Ren, Chunhui Jiang, Xinjiao Gao, Zexian Liu, Zineng Yuan, Changjiang Jin, Longping Wen, Zhaolei Zhang, Yu Xue and Xuebiao Yao.
Mol Cell Proteomics. 2010;9(4):623-634

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

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.

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.

MPTM 1.0 – Mining Protein post-Translational Modifications from literature

MPTM 1.0

:: DESCRIPTION

MPTM is a web-based text mining tool that extracts and incorporates comprehensive knowledge about post-translational modification with their underlying substrate,enzyme,site,disease,and etc. This tool integrates available data not only from the published literature but also from the biological databases. Currently, users can browse the web server MPTM and see the results by entering the name of protein or other terms. Moreover, users can download data in the MPTMDB. In addition, using the “Interaction Search” to find potential substrate-enzyme associations.

::DEVELOPER

HI_Lab @ USTC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Sun D, Wang M, Li A.
MPTM: A tool for mining protein post-translational modifications from literature.
J Bioinform Comput Biol. 2017 Oct;15(5):1740005. doi: 10.1142/S0219720017400054. Epub 2017 Sep 11. PMID: 28982288.

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.

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.