FunCoup 4.0 – Explore comprehensive Protein networks of Functional Coupling

FunCoup 4.0

:: DESCRIPTION

FunCoup (functional coupling) is a framework to infer genome-wide functional couplings in 17 model organisms. Functional coupling, or functional association, is an unspecific form of association that encompasses direct physical interaction but also more general types of direct or indirect interaction like regulatory interaction or participation the same process or pathway.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

  NO

:: MORE INFORMATION

Citation

FunCoup 4: new species, data, and visualization.
Ogris C, Guala D, Sonnhammer ELL.
Nucleic Acids Res. 2018 Jan 4;46(D1):D601-D607. doi: 10.1093/nar/gkx1138.

NetworkBLAST / Networkblast-M – Comparative Analysis of Protein Networks

NetworkBLAST / Networkblast-M

:: DESCRIPTION

NetworkBLAST analyzes protein interaction networks across species to infer protein complexes that are conserved in evolution.

For comparing multiple networks use Networkblast-M;

::DEVELOPER

Prof. Roded Sharan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NetworkBLAST / Networkblast-M

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 15;24(4):594-6. doi: 10.1093/bioinformatics/btm630. Epub 2008 Jan 2.
NetworkBLAST: comparative analysis of protein networks.
Kalaev M1, Smoot M, Ideker T, Sharan R.

protein hypernetworks 1.0.2 – Logic Framework for Interaction Dependencies in Protein Networks

proteinhypernetworks 1.0.2

:: DESCRIPTION

Protein Hypernetworks is a framework for modelling protein networks including boolean interaction dependencies.

::DEVELOPER

Johannes Köster, Eli Zamir (MPI Dortmund), Sven Rahmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java 

:: DOWNLOAD

 proteinhypernetworks

:: MORE INFORMATION

Citation

Johannes Köster, Eli Zamir, Sven Rahmann.
Protein Hypernetworks: a Logic Framework for Interaction Dependencies and Perturbation Effects in Protein Networks;

CPNM – Context-specific Protein Network Miner

CPNM

:: DESCRIPTION

CPNM is a tool that mines from PubMed networks of interacting genes/proteins based on user-context of interest (defined by a set of keywords/keyphrases).

::DEVELOPER

CPNM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(4):e34480. doi: 10.1371/journal.pone.0034480. Epub 2012 Apr 6.
Context-specific protein network miner–an online system for exploring context-specific protein interaction networks from the literature.
Chowdhary R1, Tan SL, Zhang J, Karnik S, Bajic VB, Liu JS.

PNNS – Protein Network Neighbor Search

PNNS

:: DESCRIPTION

PNNS allows the user to quickly find nodes closest to a queried vertex in any protein network available from BioGRID or specified by the user.

::DEVELOPER

Computational Biology Laboratory – Boston University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  PNNS

:: MORE INFORMATION

Citation

BMC Syst Biol. 2009 Nov 29;3:112. doi: 10.1186/1752-0509-3-112.
Spectral affinity in protein networks.
Voevodski K, Teng SH, Xia Y.

AminoNet 2.0 – Create, Visualize and Analyse Protein Network

AminoNet 2.0

:: DESCRIPTION

AMINONET is a Java-based software tool to construct different protein contact networks (unweighted and weighted; long range, short range and any range; hydrophobic, hydrophilic, charged or all-amino-acid networks). The networks thus constructed can be visualized. The software will also help in the calculation of the values of the different topological parameters of the constructed networks.

::DEVELOPER

 Md. Aftabuddin, Sudip Kundu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 AminoNet

:: MORE INFORMATION

Citation

Md. Aftabuddin and S. Kundu
AMINONET – a tool to construct and visualize amino acid networks, and to calculate topological parameters
J. Appl. Cryst. (2010). 43, 367-369