Table 4.
The Most Popular Available Tools for Analyzing and Visualizing Protein-Protein Interaction Networks with Brief Descrip-tions and References. OS Column Shows Operating System(s) Including Linux (Lin), Macintosh (Mac) and Windows (Win) that the Tools Can Run on it (Them). The Popularity of Tools Range from One Star to Five Stars Based on the Numbers of Corresponding Publications’ Citations (According to Google Scholar at the Time of Writing this Manuscript, May 2013): One Star Means Less than 50 Citations; Two Stars Mean Between 50 and 100 Citations; Three Stars Mean Be-tween 100 and 200 Citations; Four Stars Mean Between 200 and 500 Citations, and Four Stars Mean Greater Than 500 Ci-tations
| Acronym | Description | OS | Availability | Popularity | Stand-alone/Web-based/Plug-in | URL and References |
|---|---|---|---|---|---|---|
| APID (Cancer Research Center) | (Agile Protein Interaction DataAnalyzer) it's an interactive web-tool that allow exploration and analysis of protein-protein interaction | Lin/Mac/Win | Free | *** | Web-based | http://bioinfow.dep.usal.es/apid/index.htm [147] |
| BiNoM | It developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. | Lin/Mac/Win | Free | ** | Cytoscape plug-in | https://binom.curie.fr/ [148] |
| BioLayout | BioLayout is a tool for visualization and clustering of biological networks in both 3D and 2D, it is compatible with Cytoscape. It also includes analytical approaches to microarray data analysis. | Lin/Mac/Win | Free | * | Stand-alone | http://www.biolayout.org. [149, 150] |
| Cerebral | It enhances Cytoscape's functionality by using extra annotation provided by the user to both automatically generate a more pathway-like representation of a network and to provide an environment for the visualization, comparison, and clustering of expression data from multiple conditions. | Lin/Mac/Win | Free | * | Cytoscape plug-in | http://www.pathogenomics.ca/cerebral/ [151] |
| Cytoscape | A powerful interactive open source network visualization tool | Lin/Mac/Win | Free | ***** | Stand-alone | http://cytoscapeweb.cytoscape.org/ [144, 146] |
| InterProSurf (University of Texas Medical Branch) | wWeb server for predicting the functional sites on a protein surface | Lin/Mac/Win | Free | * | Web-based | http://curie.utmb.edu/prosurf.html [152] |
| InterViewer (Inha University) | Produces a molecular interaction network of good quality without computing force between every pair of nodes | Win | Free | * | Stand-alone | http://interviewer.inha.ac.kr/ [153] |
| iSPOT (Universita di Roma) | SPOT (Sequence Prediction Of Target) infer the peptide binding specificity of any member of a family of protein binding domains. | Lin/Mac/Win | Free | * | Web-based | http://cbm.bio.uniroma2.it/ispot/[154] |
| MCODE | It finds clusters (highly interconnected regions) in a network. It can also be used to lay out any graph that requires stratification according to some characteristic and thus can be used by researchers in a variety of fields | Lin/Mac/Win | Free | ***** | Cytoscape plug-in | http://baderlab.org/Software/MCODE [155] |
| Medusa | An powerful interactive tool for visualization and clustering analysis of biological networks. | Lin/Mac/Win | Free | * | Stand-alone | https://sites.google.com/site/medusa3visualization[156] |
| meta-PPISP (Florida State University) | A web server for protein-protein interaction site prediction (this tool is built on three individual web servers: cons-PPISP, PINUP, and Promate). | Lin/Mac/Win | Free | ** | Web-based | http://pipe.scs.fsu.edu/meta-ppisp.html [157] |
| NAViGaTOR (University of Toronto) |
Software package for visualizing and analyzing protein-protein interaction networks | Lin/Mac/Win | Free | ** | Stand-alone | http://ophid.utoronto.ca/navigator/ [158] |
| NOXclass (Max-Planck-Institut fur Informatik) | A classifier identifying protein-protein interaction types implemented using a SVM algorithm. | Lin/Mac/Win | Free | *** | Web-based | http://noxclass.bioinf.mpi-inf.mpg.de/ [159] |
| Osprey | a A tool for visualization and manipulation of complex interaction networks | Lin/Mac/Win | Free (registeration is needed) | **** | Stand-alone | http://biodata.mshri.on.ca/osprey/servlet/Index [160] |
| Pajek | is a standalone application, iIt can use for analyzing large networks with up to million of nodes and vertices. | Win | Free | ***** | Stand-alone | http://vlado.fmf.uni-lj.si/pub/networks/pajek/ [161, 162] |
| PathBLAST (Whitehead Institute) | It ssearches the protein-protein interaction network of the target organism to extract all protein interaction pathways that align with a pathway query. | Lin/Mac/Win | Free | **** | Web-based | http://www.pathblast.org/ [163] |
| SCOWLP (TU Dresden) | Structural classification of protein binding regions for atomic comparative analysis of protein interactions allow individual and comparative analysis of protein interactions. | Lin/Mac/Win | Free | * | Web-based | http://www.scowlp.org/scowlp/ [164, 165] |
| UVCLUSTER | Iterative cluster analysis of protein interaction data. | Lin/Win | Free for academic users (fulfillment of software license agreement is needed) | *** | Stand-alone | http://www.uv.es/genomica/UVCLUSTER/ [166] |
| VisANT | It designed specifically for the integrative visual data-mining of multi-scale Bio-Network/Pathways. It also can find the over-represented GO terms in network modules. | Lin/Mac/Win | Free | ** | Cytoscape plug-in | http://visant.bu.edu/ [167] |