LabCaS – Prediction of the Calpain Substrate Cleavage Sites

LabCaS

:: DESCRIPTION

LabCaS  (Labeling Calpain substrate cleavage Sites) is a new computational approach for accurate prediction of the calpain substrate cleavage sites from amino acid sequences.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Proteins. 2013 Apr;81(4):622-34. doi: 10.1002/prot.24217. Epub 2012 Dec 24.
LabCaS: labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields.
Fan YX1, Zhang Y, Shen HB.

Cascleave – Caspase Substrate Cleavage Site Prediction

Cascleave

:: DESCRIPTION

Cascleave is a novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates.

::DEVELOPER

Cascleave team

:: SCREENSHOTS

Cascleave

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets.
Wang M, Zhao XM, Tan H, Akutsu T, C Whisstock J, Song J.
Bioinformatics (2014) 30 (1): 71-80. doi: 10.1093/bioinformatics/btt603

KSP-PUEL – Predicting novel Substrates of Kinases of Interest

KSP-PUEL

:: DESCRIPTION

Positive-unlabeled ensemble learning (PUEL) for kinase substrate prediction (KSP-PUEL) is an application developed for predicting novel substrates of kinases of interest.

::DEVELOPER

Pengyi Yang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • JRE/ R

:: DOWNLOAD

 KSP-PUEL

:: MORE INFORMATION

Citation

Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data.
Yang P, Humphrey SJ, James DE, Yang YH, Jothi R.
Bioinformatics. 2015 Sep 22. pii: btv550

ScanSite 3 – Kinase-substrate Interaction Prediction and Short Linear Sequence Motif Discover

ScanSite 3

:: DESCRIPTION

Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

::DEVELOPER

ScanSite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.
Obenauer JC, Cantley LC, Yaffe MB.
Nucleic Acids Res. 2003 Jul 1;31(13):3635-41.

TrSSP – Transporter Substrate Specificity Prediction Server

TrSSP

:: DESCRIPTION

TrSSP is an integrative Support Vector Machine (SVM) based transporter substrate specificity predictor that is based on primary sequence information such as amino acid composition, AAIndex composition and PSSM profiles.

::DEVELOPER

The Zhao Bioinformatics Laboratory

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prediction of membrane transport proteins and their substrate specificities using primary sequence information.
Mishra NK, Chang J, Zhao PX.
PLoS One. 2014 Jun 26;9(6):e100278. doi: 10.1371/journal.pone.0100278

PSEA – Kinase-specific Prediction and analysis of Human Phosphorylation Substrates

PSEA

:: DESCRIPTION

PSEA (Phosphorylation Set Enrichment Analysis) is a software to detect new sites phosphorylated by a specific kinase, kinase family and kinase group.

::DEVELOPER

the Qiu Lab. NanChang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Sci Rep. 2014 Mar 31;4:4524. doi: 10.1038/srep04524.
PSEA: Kinase-specific prediction and analysis of human phosphorylation substrates.
Suo SB, Qiu JD, Shi SP, Chen X, Liang RP.

Predikin – Predict Substrate Specificity of Protein Kinases

Predikin

:: DESCRIPTION

Predikin is a system to predict substrate specificity of protein kinases.

::DEVELOPER

Kobe Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

   NO

:: MORE INFORMATION

Citation

The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information.
Saunders NF, Kobe B.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W286-90. doi: 10.1093/nar/gkn279