CPhos 1.0.5 – Calculate and Visualize Evolutionarily Conserved Functional Phosphorylation Sites

CPhos 1.0.5

:: 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.

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.

ViralPhos – Predict Phosphorylation Sites on Virus Proteins

ViralPhos

:: DESCRIPTION

ViralPhos is a web server for identifying potential virus phosphorylation sites with substrate motifs.

::DEVELOPER

CSB Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 16:S10. doi: 10.1186/1471-2105-14-S16-S10. Epub 2013 Oct 22.
ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins.
Huang KY, Lu CT, BBretaña N, Lee TY, Chang TH.

DisPhos 1.3 – Disorder-Enhanced Phosphorylation Sites Predictor

DisPhos 1.3

:: DESCRIPTION

DisPhos is a web tool that probabilistically determines whether a residue in a protein is phosphorylated. DisPhos predicts serine, threonine and tyrosine phosphorylation sites.

::DEVELOPER

The Center for Data Analytics and Biomedical Informatics (DABI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Feb 11;32(3):1037-49. Print 2004.
The importance of intrinsic disorder for protein phosphorylation.
Iakoucheva LM1, Radivojac P, Brown CJ, O’Connor TR, Sikes JG, Obradovic Z, Dunker AK.

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.

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.

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.

KinasePhos 2.0 – Predict Phosphorylation Sites within given Protein Sequences

KinasePhos 2.0

:: DESCRIPTION

KinasePhos is to computationally predict phosphorylation sites within given protein sequences. The known phosphorylation sites are categorized by substrate sequences and their corresponding protein kinase classes. Profile Hidden Markov Model (HMM) is applied for learning to each group of sequences surrounding to the phosphorylation residues. By comparing to other approaches previously developed, our method has higher accuracy and provides not only the location of the phosphorylation sites, but also the corresponding catalytic protein kinases

::DEVELOPER

Molecular Bioinformatics Center,  National Chiao Tung University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.
Wong YH, Lee TY, Liang HK, Huang CM, Wang TY, Yang YH, Chu CH, Huang HD, Ko MT, Hwang JK.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W588-94.

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

Phos3D Team

:: 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.