Tag: Protein Interaction Networks

NetAligner 1.0 – Fast and Accurate Alignment of Protein Interaction Networks

NetAligner 1.0

:: 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

Structural Bioinformatics and Network Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Winodows / Linux / MacOsX

:: DOWNLOAD

NetAligner

:: 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.

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.

PNmerger 1.0 – Merge Biological Pathways and Protein Interaction Networks

PNmerger 1.0

:: DESCRIPTION

PNmerger (biological Pathway and protein Netwrok merge) is a java based plug-in for the widely used open-source Cytoscape molecular interaction viewer.

::DEVELOPER

Li Dong

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / MacOs
  • Java
  • Cytoscape

:: DOWNLOAD

  PNmerger

:: MORE INFORMATION

Citation

Sun, H.; Li, D.; Wang, J.; Liu, Z.; Zhu, Y.; Xie, H.; He, F.,
Nmerger: a Cytoscape plugin to merge biological pathways and protein interaction networks.
Progress in Biochemistry and Biophysics. Accepted.

PPICompare 1.04 – Detection of Rewiring Events in Protein Interaction Networks

PPICompare 1.04

:: DESCRIPTION

PPICompare detects statistically significant rewiring events in protein-protein interaction networks – even if they are caused by alternative splicing – and reports plenty of information to that.

::DEVELOPER

Chair of Computational Biology at the Saarland University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

PPICompare 

:: MORE INFORMATION

Citation

Will T, Helms V.
Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare.
BMC Syst Biol. 2017 Apr 4;11(1):44. doi: 10.1186/s12918-017-0400-x. PMID: 28376810; PMCID: PMC5379774.

DualAligner v1.0 – Dual Alignment-based Strategy to Align Protein Interaction Networks

DualAligner v1.0

:: 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.

FACETS v1.0 – Multi-faceted Functional Decomposition of Protein Interaction Networks

FACETS v1.0

:: 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.

PinSnps – Structural and Functional analysis of SNPs in the Context of Protein Interaction Networks

PinSnps

:: DESCRIPTION

PinSnps is an interactive tool for the analysis of common variants, disease-related single-nucleotide polymorphisms (SNPs), Post-Translational Modifications (PTMs) and related functional sites mapped onto human protein interaction networks. One can search for and retrieve information about SNPs data and interacting proteins of the query.

::DEVELOPER

Fraternali lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Lu HC, Herrera Braga J, Fraternali F.
PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks.
Bioinformatics. 2016 Aug 15;32(16):2534-6. doi: 10.1093/bioinformatics/btw153. Epub 2016 Mar 24. PMID: 27153707; PMCID: PMC4978923.

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.