PhosphoSVM – Non-kinase-specific Phosphorylation site Prediction tool

PhosphoSVM

:: DESCRIPTION

PhosphoSVM is a web server for prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine.

::DEVELOPER

System Biology Laboratory Of Chi Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Amino Acids. 2014 Jun;46(6):1459-69. doi: 10.1007/s00726-014-1711-5. Epub 2014 Mar 13.
PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine.
Dou Y1, Yao B, Zhang C.

PhosphoRice 1.1.1 – Meta-predictor of Rice-specific Phosphorylation Site

PhosphoRice 1.1.1

:: DESCRIPTION

PhosphoRice, a meta-predictor of rice-specific phosphorylation site, was constructed by integrating the newly phosphorylation sites predictors, NetPhos2.0, NetPhosK, Kinasephos, Scansite, Disphos and Predphosphos with parameters selected by restricted grid search and random search

::DEVELOPER

Huaqin He’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 PhosphoRice

:: MORE INFORMATION

Citation

Plant Methods. 2012 Feb 3;8:5. doi: 10.1186/1746-4811-8-5.
PhosphoRice: a meta-predictor of rice-specific phosphorylation sites.
Que S1, Li K, Chen M, Wang Y, Yang Q, Zhang W, Zhang B, Xiong B, He H.

PhosTryp – Phosphorylation Site prediction in Trypanosomatidae

PhosTryp

:: DESCRIPTION

PhosTryp is a web tool specifically designed for the identification of phosphorylation sites in Trypanosomatids protein sequences.

::DEVELOPER

PhosTryp team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2011 Dec 19;12:614. doi: 10.1186/1471-2164-12-614.
PhosTryp: a phosphorylation site predictor specific for parasitic protozoa of the family trypanosomatidae.
Palmeri A1, Gherardini PF, Tsigankov P, Ausiello G, Späth GF, Zilberstein D, Helmer-Citterich M.

CPhos 1.3 – Calculate and Visualize Evolutionarily Conserved Functional Phosphorylation Sites

CPhos 1.3

:: DESCRIPTION

CPhos utilizes an information theory-based algorithm to assess the conservation of phosphorylation sites among species. A conservation established from this approach can be used to potentially assess the functional significance of a particular phosphorylation site.

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

CPhos

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

CPhos

:: MORE INFORMATION

Citation

CPhos: a program to calculate and visualize evolutionarily conserved functional phosphorylation sites.
Zhao B, Pisitkun T, Hoffert JD, Knepper MA, Saeed F.
Proteomics. 2012 Nov;12(22):3299-303. doi: 10.1002/pmic.201200189.

PhosSA – Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data

PhosSA

:: DESCRIPTION

PhosSA is a program for phosphorylation site assignment of LC-MS/MS data. It uses a linear-time and linear space dynamic programming strategy for phosphorylation site assignment. The algorithm optimizes the objective function defined as the summation of intensity peaks that are associated with theoretical peptide fragmentation ions. A classifier introduced in the algorithm exploits the specific characteristics of mass spectrometry data to distinguish between the correctly and incorrectly assigned site(s).

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

PhosSA

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

PhosSA

:: MORE INFORMATION

Citation

Proteome Sci. 2013 Nov 7;11(Suppl 1):S14. doi: 10.1186/1477-5956-11-S1-S14. Epub 2013 Nov 7.
PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data.
Saeed F, Pisitkun T, Hoffert JD, Rashidian S, Wang G, Gucek M, Knepper MA.

PPSP 1.06 – Prediction of PK-Specific Phosphorylation Site

PPSP 1.06

:: DESCRIPTION

PPSP  is a novel, versatile and comprehensive program which deployed with approach of Bayesian decision theory (BDT). PPSP could predict the potential phosphorylation sites accurately for approximately 70 PK (Protein Kinase) groups.

::DEVELOPER

PPSP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Mar 20;7:163.
PPSP: prediction of PK-specific phosphorylation site with Bayesian decision theory.
Xue Y, Li A, Wang L, Feng H, Yao X.

iPhos-PseEn – Predict the identifying human Phosphorylation Sites

iPhos-PseEn

:: DESCRIPTION

iPhos-PseEn is a predictor by fusing four different pseudo component approaches (amino acids’ disorder scores, nearest neighbors, occurrence frequencies, and position weights) into an ensemble classifier via a voting system to identify human phosphorylation sites.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Oncotarget. 2016 Aug 9;7(32):51270-51283. doi: 10.18632/oncotarget.9987.
iPhos-PseEn: identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier
Wang-Ren Qiu 1 2, Xuan Xiao 1 3, Zhao-Chun Xu 1, Kuo-Chen Chou 3 4 5

Phos3D – Prediction of Phosphorylation Sites (P-sites) in Proteins

Phos3D

:: DESCRIPTION

Phos3D is a web server for the prediction of phosphorylation sites (P-sites) in proteins. The approach is based on Support Vector Machines trained on sequence profiles enhanced by information from the spatial context of experimentally identified P-sites.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Apr 21;10:117.
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins.
Durek P, Schudoma C, Weckwerth W, Selbig J, Walther D.

NetPhos 3.1 – Generic Phosphorylation Sites in Eukaryotic Proteins

NetPhos 3.1

:: DESCRIPTION

NetPhos produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetPhos

:: MORE INFORMATION

Citation

Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites.
Blom, N., Gammeltoft, S., and Brunak, S.
Journal of Molecular Biology: 294(5): 1351-1362, 1999.

PhosPatch – Phosphorylation Site Patch Analysis

PhosPatch

:: DESCRIPTION

PhosPatch is a tool to analyse the charge and accessibility around potential phosphorylation sites

::DEVELOPER

Warwicker Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Fortron

:: DOWNLOAD

   PhosPatch

:: MORE INFORMATION

Citation

Kitchen J et al (2008)
Charge environments around phosphorylation sites in proteins.
BMC Structural Biology 8:19