PLW – Detecting Protein Complexes from Protein Interaction Networks

PLW

:: DESCRIPTION

PLW (Probabilistic Local Walks) is a graph clustering algorithm, and was designed to detect protein complexes in protein-protein interaction (PPI) networks with high accuracy and efficiency.

::DEVELOPER

PLW team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX

:: DOWNLOAD

PLW

:: MORE INFORMATION

Citation

BMC Genomics. 2013;14 Suppl 5:S15. doi: 10.1186/1471-2164-14-S5-S15. Epub 2013 Oct 16.
PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks.
Wong D, Li XL, Wu M, Zheng J, Ng SK.

ComplexCorr – Predict the Connectivity of Subunits within large Protein Complexes

ComplexCorr

:: DESCRIPTION

With ComplexCorr you can predict the connectivity of subunits within large protein complexes.

::DEVELOPER

ComplexCorr team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

J Mol Biol. 2010 Nov 19;404(1):158-71. doi: 10.1016/j.jmb.2010.09.029. Epub 2010 Sep 22.
Coevolution predicts direct interactions between mtDNA-encoded and nDNA-encoded subunits of oxidative phosphorylation complex i.
Gershoni M1, Fuchs A, Shani N, Fridman Y, Corral-Debrinski M, Aharoni A, Frishman D, Mishmar D.

TSN-PCD / DFM-CIN – Identify Protein Complexes / Functional Modules from these TSNs

TSN-PCD / DFM-CIN

:: DESCRIPTION

The algorithm TSN-PCD was developed to identify protein complexes from these TSNs (time-sequenced subnetworks).

DFM-CIN is proposed to discover functional modules based on the identified complexes.

::DEVELOPER

CSU-Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

TSN-PCD / DFM-CIN

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 May 23;13:109. doi: 10.1186/1471-2105-13-109.
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data.
Li M1, Wu X, Wang J, Pan Y.

PEWCC – Identify Protein Complexes from PPI

PEWCC

:: DESCRIPTION

PEWCC is a novel graph mining algorithm to identify protein complexes from protein-protein interaction data.

::DEVELOPER

Nazar Zaki , Bioinformatics Laboratory, UAE University.

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows / Linux/ MacOsX
Python

:: DOWNLOAD

PEWCC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 May 20;14:163. doi: 10.1186/1471-2105-14-163.
Protein complex detection using interaction reliability assessment and weighted clustering coefficient.
Zaki N, Efimov D, Berengueres J.

ClusterONE 1.0 – Detecting Overlapping Protein Complexes in Protein-protein Interaction Networks

ClusterONE 1.0

:: DESCRIPTION

ClusterONE (Clustering with Overlapping Neighborhood Expansion) is a graph clustering algorithm that is able to handle weighted graphs and readily generates overlapping clusters. Owing to these properties, it is especially useful for detecting protein complexes in protein-protein interaction networks with associated confidence values.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows/ Linux / MacOsX
Java

:: DOWNLOAD

ClusterONE

:: MORE INFORMATION

Citation

Nat Methods. 2012 Mar 18;9(5):471-2. doi: 10.1038/nmeth.1938.
Detecting overlapping protein complexes in protein-protein interaction networks.
Nepusz T1, Yu H, Paccanaro A.