SAPIN – Structural Analysis of Protein Interaction Networks

SAPIN

:: DESCRIPTION

SAPIN is a framework dedicated to the Structural Analysis of Protein Interaction Networks.SAPIN first identifies the protein parts that could be involved in the interaction and provides template structures. Next, SAPIN performs structural superimpositions to identify compatible and mutually exclusive interactions. Finally, the results are displayed using Cytoscape Web.

::DEVELOPER

Design of Biological Systems Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2998-9. doi: 10.1093/bioinformatics/bts539. Epub 2012 Sep 6.
SAPIN: a framework for the structural analysis of protein interaction networks.
Yang JS1, Campagna A, Delgado J, Vanhee P, Serrano L, Kiel C.

TORQUE – Topology-Free Querying of Protein Interaction Networks

TORQUE

:: DESCRIPTION

TORQUE is a tool for cross-species querying of protein-protein interaction networks. Given a complex (set of proteins) for a query species, Torque seeks a matching set of proteins of a target species that are sequence-similar to the query proteins and span a connected region of the target network.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TORQUE: topology-free querying of protein interaction networks.
Bruckner S, Hüffner F, Karp RM, Shamir R, Sharan R.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W106-8. doi: 10.1093/nar/gkp474.

CELLmicrocosmos 4.2 PathwayIntegration – Localization and Visualization of Protein-Interaction Networks in a Virtual Cell

CELLmicrocosmos 4.2 PathwayIntegration

:: DESCRIPTION

The CELLmicrocosmos PathwayIntegration (CmPI) was developed to support and visualize the subcellular localization prediction of protein-related data such as protein-interaction networks.

::DEVELOPER

the Bioinformatics / Medical Informatics department at Bielefeld University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 CmPI

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Feb;11(1):1340005. doi: 10.1142/S0219720013400052. Epub 2013 Feb 18.
Subcellular localization charts: a new visual methodology for the semi-automatic localization of protein-related data sets.
Sommer B1, Kormeier B, Demenkov PS, Arrigo P, Hippe K, Ates Ö, Kochetov AV, Ivanisenko VA, Kolchanov NA, Hofestädt R.

FACETS 20130201 – Multi-faceted Functional Decomposition of Protein Interaction Networks

FACETS 20130201

:: DESCRIPTION

FACETS is a data-driven and generic algorithm for generating multi-faceted functional decompositions of a PPI network, providing multiple perspectives of the functional organization landscape of the network.

::DEVELOPER

Computational Systems Biology Research Group(COSBY)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

FACETS

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Oct 15;28(20):2624-31. doi: 10.1093/bioinformatics/bts469. Epub 2012 Aug 20.
FACETS: multi-faceted functional decomposition of protein interaction networks.
Seah BS1, Bhowmick SS, Dewey CF Jr.

DualAligner 20131129 – Dual Alignment-based Strategy to Align Protein Interaction Networks

DualAligner 20131129

:: DESCRIPTION

DualAligner performs dual network alignment, in which both region-to-region alignment, where whole subgraph of one network is aligned to subgraph of another, and protein-to-protein alignment, where individual proteins in networks are aligned to one another, are performed to achieve higher accuracy network alignments.

::DEVELOPER

Computational Systems Biology Research Group(COSBY)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

DualAligner

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 28. pii: btu358. [Epub ahead of print]
DualAligner: A Dual Alignment-based Strategy to Align Protein Interaction Networks.
Seah BS1, Bhowmick SS2, Dewey CF Jr3.

PerturbationAnalyzer 1.2 – Investigating the Effects of Concentration Perturbation on Protein Interaction Networks

PerturbationAnalyzer 1.2

:: DESCRIPTION

The PerturbationAnalyzer is an open source Java plugin for Cytoscape to evaluate the propagation effects on interaction networks by comparing the equilibrium states before and after certain perturbation. Given an interaction network and initial parameters, the PerturbationAnalyzer finds the equilibrium state governed by the law of mass action (LMA) for protein binding network, and generates a customizable view to provide an intuitive visual representation of the result of the propagation effect on the network.

::DEVELOPER

PerturbationAnalyzer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 PerturbationAnalyzer

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 15;26(2):275-7. doi: 10.1093/bioinformatics/btp634. Epub 2009 Nov 13.
PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks.
Li F1, Li P, Xu W, Peng Y, Bo X, Wang S.

PLW – Detecting Protein Complexes from Protein Interaction Networks

PLW

:: DESCRIPTION

PLW (Probabilistic Local Walks) is a graph clustering algorithm, and was designed to detect protein complexes in protein-protein interaction (PPI) networks with high accuracy and efficiency.

::DEVELOPER

PLW team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 PLW

:: MORE INFORMATION

Citation

BMC Genomics. 2013;14 Suppl 5:S15. doi: 10.1186/1471-2164-14-S5-S15. Epub 2013 Oct 16.
PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks.
Wong D, Li XL, Wu M, Zheng J, Ng SK.

NetAligner – Fast and Accurate Alignment of Protein Interaction Networks

NetAligner

:: DESCRIPTION

NetAligner is a novel network alignment tool that allows the identification of conserved protein complexes and pathways across organisms, providing valuable hints as to how those interaction networks evolved.

::DEVELOPER

Institute for Research in Biomedicine (IRB) Barcelona

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W157-61. doi: 10.1093/nar/gks446. Epub 2012 May 22.
NetAligner–a network alignment server to compare complexes, pathways and whole interactomes.
Pache RA1, Céol A, Aloy P.

Graemlin 2.01 – Aligning Multiple Global Protein Interaction Networks

Graemlin 2.01

:: DESCRIPTION

Graemlin is a tool for aligning multiple global protein interaction networks; Graemlin also supports search for homology between a query module of proteins and a database of interaction networks.

::DEVELOPER

Serafim Batzoglou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Graemlin

:: MORE INFORMATION

Citation

Graemlin: general and robust alignment of multiple large interaction networks.
Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S.
Genome Res. 2006 Sep;16(9):1169-81