:: 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
:: DOWNLOAD
:: MORE INFORMATION
Citation
Johannes Köster, Eli Zamir, Sven Rahmann.
Protein Hypernetworks: a Logic Framework for Interaction Dependencies and Perturbation Effects in Protein Networks;
:: 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
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.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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.
:: 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
:: DOWNLOAD
:: 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