ArchKI – Classification of common Functional Loops of Kinase Super-families

ArchKI

:: DESCRIPTION

ArchKI is a structural classification of kinase loops with information of functional residues. We are interested in finding relationships between structure and function of classified kinase-loops using three different sources of functional information: (i) functional residues (or regions) described in the literature (ii) residues described in the SITE records of the pdb files that specify residues comprising catalytic, cofactor, anticodon, regulatory or other important sites and (iii) residues in contact with heteroatoms.

::DEVELOPER

ArchKI Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Proteins. 2004 Aug 15;56(3):539-55.
Classification of common functional loops of kinase super-families.
Fernandez-Fuentes N, Hermoso A, Espadaler J, Querol E, Aviles FX, Oliva B.

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

IKAP – Inference of Kinase Activities from Phosphoproteomics

IKAP

:: DESCRIPTION

IKAP is a heuristic framework for inference of kinase activities from Phosphoproteomics data.

::DEVELOPER

IKAP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • MatLab

:: DOWNLOAD

 IKAP

:: MORE INFORMATION

Citation:

IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data.
Mischnik M, Sacco F, Cox J, Schneider HC, Schäfer M, Hendlich M, Crowther D, Mann M, Klabunde T.
Bioinformatics. 2015 Dec 1. pii: btv699.

ScanSite 4.0 – Kinase-substrate Interaction Prediction and Short Linear Sequence Motif Discover

ScanSite 4.0

:: 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.

KEA2 – Kinase Enrichment Analysis

KEA2

:: DESCRIPTION

KEA is a web-based tool with an underlying database providing users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them. The system draws from several available kinase-substrate databases to computes kinase enrichment probability based on the distribution of kinase-substrate proportions in the background kinase-substrate database compared with kinases found to be associated with an input list of genes/proteins.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

KEA

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

Citation

Bioinformatics. 2009 Mar 1;25(5):684-6. doi: 10.1093/bioinformatics/btp026. Epub 2009 Jan 28.
KEA: kinase enrichment analysis.
Lachmann A, Ma’ayan A.

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

GPS-Polo 1.0 – Prediction for Polo-like kinases

GPS-Polo 1.0

:: DESCRIPTION

GPS-Polo is a software for prediction for polo-like kinases.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows / Linux / MacOsX
  • Java

:: DOWNLOAD

 GPS-Polo

:: MORE INFORMATION

Citation

Systematic analysis of PLK-mediated phosphoproteome in eukaryotes.
Zexian Liu, Jian Ren, Jun Cao, Jiang He, Xuebiao Yao, Changjiang Jin and Yu Xue.
Brief Bioinform (2012) doi: 10.1093/bib/bbs041