ICSearcher – Identifying Protein Complexes in PPI networks

ICSearcher

:: DESCRIPTION

ICSearcher is a tool which is based on BMM(the algorithm Based on the new Modularity function for Merging modules) for identifying protein complexes.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

ICSearcher

:: MORE INFORMATION

 

PLSMC – Identifying Protein Complexes in PPI Network

PLSMC

:: DESCRIPTION

PLSMC is a novel algorithm based on a penalized least square method to detect complex in PPI network. PLSMC is to minimize the distances between the interaction and co-complex of protein pairs.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

PLSMC

:: MORE INFORMATION

Citation

A least square method based model for identifying protein complexes in protein-protein interaction network.
Dai Q, Guo M, Guo Y, Liu X, Liu Y, Teng Z.
Biomed Res Int. 2014;2014:720960. doi: 10.1155/2014/720960.

IsoRank 2008 / IsoRankN 2009 – Global Alignment of multiple PPI Networks / on Spectral methods

IsoRank 2008 / IsoRankN 2009

:: DESCRIPTION

IsoRank is an algorithm for global alignment of multiple protein-protein interaction (PPI) networks. The intuition is that a protein in one PPI network is a good match for a protein in another network if the former’s neighbors are good matches for the latter’s neighbors.

IsoRankN (IsoRank-Nibble) is a global multiple-network alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks.

::DEVELOPER

Bonnie Berger‘s group at MIT.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

IsoRank / IsoRankN

:: MORE INFORMATION

Citation:

Global alignment of multiple protein interaction networks with application to functional orthology detection.
Singh R, Xu J, Berger B.
Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12763-8. doi: 10.1073/pnas.0806627105.

IsoRankN: spectral methods for global alignment of multiple protein networks.
Liao CS, Lu K, Baym M, Singh R, Berger B.
Bioinformatics. 2009 Jun 15;25(12):i253-8. doi: 10.1093/bioinformatics/btp203.

CoAch – COre-AttaCHment based Complex Mining

CoAch

:: DESCRIPTION

CoAch: A Core-Attachment based Method to Detect Protein Complexes in PPI Networks

::DEVELOPER

Xiaoli Li, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Windows

:: DOWNLOAD

 CoAch

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jun 2;10:169. doi: 10.1186/1471-2105-10-169.
A core-attachment based method to detect protein complexes in PPI networks.
Wu M1, Li X, Kwoh CK, Ng SK.

Core 0.10 – Predict Protein Complex from PPI network

Core 0.10

:: DESCRIPTION

Core is an open source program for predicting protein complex from PPI network.

::DEVELOPER

Bioinformatics Research Group of Hong Kong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Core

:: MORE INFORMATION

Citation:

Predicting protein complexes from PPI data: a core-attachment approach.
Leung HC, Xiang Q, Yiu SM, Chin FY.
J Comput Biol. 2009 Feb;16(2):133-44.