Tag: Protein-Protein Interaction Networks

ModuleAlign – Module-based Global Alignment of Protein-protein Interaction networks

ModuleAlign

:: DESCRIPTION

ModuleAlign uses a novel scoring scheme that integrates sequence information and both local and global network topology. It computes a homology score between proteins based on a hierarchical clustering of the input networks. (a) shows the hierarchical structure of a network. Leaves represent the proteins and each cluster joins sets of proteins with similar interactions.

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ModuleAlign

:: MORE INFORMATION

Citation:

Hashemifar S, Ma J, Naveed H, Canzar S, Xu J.
ModuleAlign: module-based global alignment of protein-protein interaction networks.
Bioinformatics. 2016 Sep 1;32(17):i658-i664. doi: 10.1093/bioinformatics/btw447. PMID: 27587686.

NETAL – Global Alignment of Protein-protein Interaction Networks

NETAL

:: DESCRIPTION

NETAL (network aligner) is a software for the global alignment of protein-protein interaction networks. It uses a greedy method, based on the alignment scoring matrix, which is derived from both biological and topological information of input networks to find the best global network alignment.

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 NETAL

:: MORE INFORMATION

Citation:

NETAL: a new graph-based method for global alignment of protein-protein interaction networks.
Neyshabur B, Khadem A, Hashemifar S, Arab SS.
Bioinformatics. 2013 Jul 1;29(13):1654-62. doi: 10.1093/bioinformatics/btt202. Epub 2013 May 21.

Pepper 1.5.1 – Protein Complex Expansion using Protein-Protein intERaction networks

Pepper 1.5.1

:: DESCRIPTION

PEPPER is a plugin which finds meaningful pathways / complexes connecting a protein set members within a PPI-network using multi-objective optimization.

::DEVELOPER

Pepper team

:: SCREENSHOTS

Pepper1

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • CytoScape

:: DOWNLOAD

 Pepper

:: MORE INFORMATION

Citation

Pepper: Cytoscape app for Protein complex Expansion using Protein-Protein intERaction networks.
Winterhalter C, Nicolle R, Louis A, To C, Radvanyi F, Elati M.
Bioinformatics. 2014 Aug 18. pii: btu517

Modulerole 1.3.1 – Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks

Modulerole 1.3.1

:: DESCRIPTION

ModuleRole is a user-friendly web server tool which finds modules in PPI network and defines the roles for every node, and produces files for visualization in Cytoscape and Pajek.

::DEVELOPER

Guipeng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Modulerole

:: MORE INFORMATION

Citation

PLoS One. 2014 May 1;9(5):e94608. doi: 10.1371/journal.pone.0094608. eCollection 2014.
ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks.
Li G, Li M, Zhang Y, Wang D, Li R, Guimerà R, Gao JT, Zhang MQ.