Tag: Protein-Protein Interaction Network

HubAlign – Alignment of Protein-protein Interaction Networks

HubAlign

:: DESCRIPTION

HubAlign is a software for the alignment of protein-protein interaction networks that is based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information.

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HubAlign

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Sep 1;30(17):i438-i444. doi: 10.1093/bioinformatics/btu450.
HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.
Hashemifar S, Xu J.

3DProIN – Protein-Protein Interaction Networks and Structure Visualization

3DProIN

:: DESCRIPTION

3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view.

::DEVELOPER

3DProIN team

:: SCREENSHOTS

3DProIN

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

 3DProIN

:: MORE INFORMATION

Citation

Am J Bioinform Comput Biol. 2014 Jun 14;2(1):32-37.
3DProIN: Protein-Protein Interaction Networks and Structure Visualization.
Li H, Liu C.

NatalieQ – Topology-based Protein-protein Interaction Network Querying

NatalieQ

:: DESCRIPTION

NatalieQ is a web server for aligning two protein-interaction networks in order to highlight conserved subnetworks. It is an interface to the more general network alignment method Natalie.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2014 Apr 1;8:40. doi: 10.1186/1752-0509-8-40.
NatalieQ: a web server for protein-protein interaction network querying.
El-Kebir M, Brandt BW, Heringa J, Klau GW.

ModuleSearch – Finding Functional Modules in Protein-protein Interaction Network

ModuleSearch

:: DESCRIPTION

ModuleSearch is a software for finding cliques and near-cliques in a protein-protein interaction network.

::DEVELOPER

Biocomputing Lab

:: SCREENSHOTS

ModuleSearch

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

 ModuleSearch

:: MORE INFORMATION

Citation

Comput Methods Biomech Biomed Engin. 2012;15(7):691-9. doi: 10.1080/10255842.2011.555404. Epub 2011 Aug 9.
ModuleSearch: finding functional modules in a protein-protein interaction network.
Cui G1, Shrestha R, Han K.

ClusterONE 1.0 – Detecting Overlapping Protein Complexes in Protein-protein Interaction Networks

ClusterONE 1.0

:: DESCRIPTION

ClusterONE (Clustering with Overlapping Neighborhood Expansion) is a graph clustering algorithm that is able to handle weighted graphs and readily generates overlapping clusters. Owing to these properties, it is especially useful for detecting protein complexes in protein-protein interaction networks with associated confidence values.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

 ClusterONE

:: MORE INFORMATION

Citation

Nat Methods. 2012 Mar 18;9(5):471-2. doi: 10.1038/nmeth.1938.
Detecting overlapping protein complexes in protein-protein interaction networks.
Nepusz T1, Yu H, Paccanaro A.

PATH2PPI 1.20.0 – Prediction of Pathway-specific Protein-protein Interaction Networks

PATH2PPI 1.20.0

:: DESCRIPTION

PATH2PPI is a package to predict pathway specific protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available.

::DEVELOPER

Molecular Bioinformatics MolBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R/BioConductor

:: DOWNLOAD

 PATH2PPI

:: MORE INFORMATION

Citation

PATH2PPI: an R package to predict protein-protein interaction networks for a set of proteins.
Philipp O, Osiewacz HD, Koch I.
Bioinformatics. 2016 Jan 5. pii: btv765.

CLAIM 20131010 – Coupling Co-expression Data and Protein-protein Interaction Networks for Functional Protein Analysis

CLAIM 20131010

:: DESCRIPTION

CLAIM (CLuster Analysis Integration Method) is a new method for integrating co-expression data obtained through microarray experiments (MA) and protein-protein interaction (PPI) network data. Microarray and PPI data are separately clustered; the clusters are then merged in a special graph; cliques of this graph would identify a group of functionally related proteins. The biological insight provided by these groups is analyzed on the basis of co-localization and mRNA developmental expression, pointing out the new information that can be obtained by this method.

::DEVELOPER

The Bioinformatics Group, Poznan University of Technology.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Complier

:: DOWNLOAD

 CLAIM

:: MORE INFORMATION

Citation

OMICS. 2014 Feb;18(2):155-65. doi: 10.1089/omi.2013.0050. Epub 2014 Jan 3.
An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics: application on Arabidopsis thaliana.
Santoni D1, Swiercz A, Zmieńko A, Kasprzak M, Blazewicz M, Bertolazzi P, Felici G.

Nascent 1.2 – Protein-Protein Physical Interaction Network Originating Tool

Nascent 1.2

:: DESCRIPTION

NASCENT is a completely automatic web-based tool and also a downloadable Java program, capable of modeling and generating protein interaction networks even for non-model organisms. The tool performs protein interaction network modeling through gene-name mapping, and outputs the resulting network in graphical form and also in computer-readable graph-forms, directly applicable by popular network modeling software.

::DEVELOPER

PIT – Protein Information Technology Group

:: SCREENSHOTS

Nascent

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 Nascent

:: MORE INFORMATION

Citation

Bioinformation. 2009 Apr 24;3(8):361-3.
NASCENT: an automatic protein interaction network generation tool for non-model organisms.
Banky D, Ordog R, Grolmusz V.