PINA 3.0 – Protein Interaction Network Analysis platform

PINA 3.0

:: DESCRIPTION

PINA is an integrated platform for protein-protein interaction network construction, filtering, analysis, visualization and management.

::DEVELOPER

Center for Cancer Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Du Y, Cai M, Xing X, Ji J, Yang E, Wu J.
PINA 3.0: mining cancer interactome.
Nucleic Acids Res. 2021 Jan 8;49(D1):D1351-D1357. doi: 10.1093/nar/gkaa1075. PMID: 33231689; PMCID: PMC7779002.

Cowley, M.J., Pinese, M., Kassahn, K.S., Waddell, N., Pearson, J.V., Grimmond, S.M., Biankin, A.V., Hautaniemi, S. and Wu, J. (2012)
PINA v2.0: mining interactome modules.
Nucleic Acids Res, 40, D862-865.

spinal 2 – Scalable Protein Interaction Network Alignment

spinal 2

:: DESCRIPTION

SPINAL is an algorithm for the problem of globally aligning a pair of PPI networks.

::DEVELOPER

Cesim Erten,Ahmet Emre Aladağ

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

spinal

:: MORE INFORMATION

Citation

SPINAL: scalable protein interaction network alignment.
Aladag AE, Erten C.
Bioinformatics (2013) 29 (7): 917-924.

PINV – Web-based Protein Interaction Network Visualizer

PINV

:: DESCRIPTION

PINV is an open source, native web application that facilitates the visualization of protein interactions

::DEVELOPER

the University of Cape Town (UCT) Computational Biology (CBIO) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

PINV

:: MORE INFORMATION

Citation

A web-based protein interaction network visualizer.
Salazar GA, Meintjes A, Mazandu GK, Rapanoël HA, Akinola RO, Mulder NJ.
BMC Bioinformatics. 2014 May 6;15:129. doi: 10.1186/1471-2105-15-129.

PPIXpress 1.23 – Specific Protein Interaction Networks from Transcript Expression

PPIXpress 1.23

:: DESCRIPTION

PPIXpress exploits expression data at the transcript-level and is thus able to also reveal alterations in protein connectivity caused by alternative splicing.

::DEVELOPER

PPIXpress team

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX / Windows
Java

:: DOWNLOAD

PPIXpress

:: MORE INFORMATION

Citation

PPIXpress: construction of condition-specific protein interaction networks based on transcript expression.
Will T, Helms V.
Bioinformatics. 2015 Oct 27. pii: btv620.

InterViewer 4.0 – Visualize Large-scale Protein Interaction Networks

InterViewer 4.0

:: DESCRIPTION

InterViewer is a software for visualizing large-scale protein interaction networks. InterViewer (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component, and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of InterViewer over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases, and (3) it provides several operations for effectively exploring large-scale protein interaction networks.

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java

:: DOWNLOAD

InterViewer

:: MORE INFORMATION

Citation

Byong-Hyon Ju, Byungkyu Park, Jong H. Park and Kyungsook Han
Visualization and analysis of protein interactions
Bioinformatics (2003) 19 (2): 317-318.

PISwap – Protein Interaction Network Alignments

PISwap

:: DESCRIPTION

PISwap is a software for optimizing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of other intractable problems.

::DEVELOPER

Leonid Chindelevitch (leonidus at mit dot edu), Bonnie Berger‘s group at MIT.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Python

:: DOWNLOAD

PISwap

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Nov 1;29(21):2765-73. doi: 10.1093/bioinformatics/btt486
Optimizing a global alignment of protein interaction networks.
Chindelevitch L, Ma CY, Liao CS, Berger B.

PathBLAST – Alignment of Protein Interaction Networks

PathBLAST

:: DESCRIPTION

PathBLAST searches the protein-protein interaction network of the target organism to extract all protein interaction pathways that align with a pathway query.

::DEVELOPER

the Ideker Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W83-8.
PathBLAST: a tool for alignment of protein interaction networks.
Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T.

PINALOG 1.0 – Protein Interaction Network Alignment

PINALOG 1.0

:: DESCRIPTION

PINALOG is a protein-protein interaction(PPI) network alignment method aiming to map similar parts of PPI networks in terms of protein similarity (by both sequence and function) and the local network similarity. PINALOG incorporates not only sequence similarity and topological similarity of proteins in the equivalencing process but also uses the function similarity of protein pairs.

::DEVELOPER

Structural Bioinformatics Group, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux

:: DOWNLOAD

PINALOG

:: MORE INFORMATION

Citation

Bioinformatics. 2012 May 1;28(9):1239-45. doi: 10.1093/bioinformatics/bts119. Epub 2012 Mar 13.
PINALOG: a novel approach to align protein interaction networks–implications for complex detection and function prediction.
Phan HT, Sternberg MJ.

Ensemble NMF 0.91 / NMF Tree Browser 0.98 – Clustering and Visualising Protein Interaction Networks

Ensemble NMF 0.91 / NMF Tree Browser 0.98

:: DESCRIPTION

Ensemble NMF (Non-negative Matrix Factorization ) is a software for clustering and visualising protein interaction networks.

The NMF Tree Browser tool is a cross-platform Java application for visually inspecting a soft hierarchy as produced by the Ensemble NMF algorithm.

::DEVELOPER

the Machine Learning Group (MLG)

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows /Mac OsX
Java / C++ Compiler

:: DOWNLOAD

Ensemble NMF / NMF Tree Browser

:: MORE INFORMATION

Citation

Greene, D., Cagney, G., Krogan, N and Cunningham, P. (2008),
“Ensemble Non-negative Matrix Factorization Methods for Clustering Protein-Protein Interactions“,
Bioinformatics, 24, 15: 1722–1728.

FASPAD 20070415 – Detection of Linear Signaling Pathways in Protein Interaction Networks

FASPAD 20070415

:: DESCRIPTION

FASPAD (Fast Signaling Pathway Detection) is a tool for the detection of linear signaling pathways in protein interaction networks.Using recent algorithmic insights, it can solve the underlying NP-hard problem quite fast: for protein networks of typical size (several thousand nodes), pathway candidates of length up to 13 proteins can be found within seconds and with a 99.9% probability of optimality. FASPAD graphically displays all candidates that are found; for evaluation and comparison purposes, an overlay of several candidates and the surrounding network context can also be shown.

::DEVELOPER

Falk Hüffner and Thomas Zichner

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

FASPAD for Linux ; for win ; Source Code

:: MORE INFORMATION

Citation

F. Hüffner, S. Wernicke, and T. Zichner.
Algorithm engineering for color-coding with applications to signaling pathway detection.
Algorithmica, 52(2):114–132, 2008