PPI Tools Comparison
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I2DIntActMINTHomoMINTSTRINGBioGRIDUniHIMENTHACPDBAPIDPINVPathway CommonsPathBLASTDominovisANTAVISDIPBioLayout Express 3DIMExCytoscapeNAViGaTORMedusaOndexPIVOTBIANAOspreyArena3DReactomeKEGGUniProtNCBINCI/PID3d-partnerICBSHPIDiHOPEnsemblSWISS-MODELPDBBioCycSIMAPDOMINEPSIbaseHUGE-PPIBindingDBiSPOTMIPSOPHIDPIPSBINDHPRDPRISMNatalieQmany other not ppi specific but protein-domain interaction as well as other systems biology or not online running tools
NameInterologous Interaction DatabaseIntAct Molecular Interaction DatabaseMolecular INTeraction databasecompare MINT - specialized version for homo sapiens of MINTSearch Tool for the Retrieval of Interacting Genes/ProteinsBiological General Repository for Interaction DatasetsUnified Human InteractomeInteractome BrowserConsensusPathDBAgile Protein Interaction DataAnalyzerProtein Interaction Network Visualizerdomain peptide interactionsIntegrative Visual Analysis Tool for Biological Networks and PathwaysDatabase of Interacting ProteinsMedusa-VisualizationProtein Interactions VisualizatiOn ToolBiologic Interaction and Network AnalysisKyoto Encyclopedia of Genes and GenomesNational Center for Biotechnology InformationNational Cancer Institute / Pathway Interaction DatabaseInter-Chain Beta-SheetsHuman Protein Interaction DatabaseInformation Hyperlinked Over ProteinsProtein Data BankBioCyc Database CollectionSimilarity Matrix of ProteinsDatabase of Protein Domain interactionsStructural Interactome Map of all ProteinsHuman Unidentified Gene-Encoded Large ProteinsBinding Database
iSpecificity Prediction Of Target

The MIPS Mammalian Protein-Protein Interaction Database
Please refer to I2D. Online Predicted Human Interaction Database (OPHID) is a web-based database of predicted interactions between human proteins.
Human Protein-Protein Interaction Prediction

Biomolecular Interaction Network Database
Human Protein Reference Database

PRISM: Protein Interactions By Structural Matching
Topology-based protein-protein interaction network querying
Has PPI Web VisualizationYesYesYesYesYesYesYesYesYesYesYesYesYesNONoNoNoNoNoNoNoNoNoNoNoNoNoNoNoNoNONoNoNodownNoNoist not a ppi tool, but a promising protein model visualization toool!NoNoNoNoNoNoNoNoNoYes, see I2DYesNoNoNoYes
Short descriptionI2D is developed and maintained by Jurisica Lab at Ontario Cancer Institute. I2D will continue to expand as new protein-protein interaction data becomes available.IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available. MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators.Tool for extended Protein-Protein interactions of the orthologous proteins in Homo sapiens.Database for known and predicted protein interactions, including direct (phsical) and indirect (functional) associations.BioGRID is an online interaction repository with data compiled through comprehensive curation efforts.Users can enter gene or protein identifiers from different organisms to obtain physical and regulatory interaction partners in the human interactome. Results are displayed by the UniHI visualisation tool which offers multiple options to filter interactions (e.g. based on source of interactions or amount of evidence).mentha archives evidence collected from different sources and presents these data in a complete and comprehensive wayThe DB integrates different types of functional interactions between physical entities in the cell like genes, RNA, proteins, protein complexes and metabolites. interaction information is collected from 30 public resourcesAn interactive bioinformatic web-tool that has been developed to allow exploration and analysis of main currently known information about protein-protein interactions integrated and unified in a common and comparative platform. PINV, an open source, native web application that facilitates the visualization of protein interactionsresearch collaborative environments. A network biology resource and acts as a convenient point of access to biological pathway information which you can search, visualize and download. - Remark: The tool does not show protein protein interactions but details about genes and their interactions extracted from multiple pathway data resources and is therefore intersting for further exploration but not in particular for the task of ppi analysis!PathBLAST searches the protein-protein interaction network of the target organism to extract all protein interaction pathways that align with a pathway query.Sub-DB of MINT: A Database for doman-peptide interactionsIntegrative Visual Analysis Tool for Biological Networks and PathwaysAVIS was featured in a Google Gadgets API Case Study. Is just an AJAX visualizaion technology but very interesting for future research.The DIP database catalogs experimentally determined interactions between proteins.Specifically designed for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not exclusively, from biological data.A database of predicted functional associations among genes and proteins in many different organisms. Created using both experimental and computational setups.Network Data Integration, Analysis, and Visualization in a BoxVisualize your graph using versatile graphics, powered with OpenGL accelerated libraries.A java standalone application for visualization and clustering analysis of biological networks in 2D; enriched with a variety of layout and clustering methods.Enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques. Ondex can be used in a number of important application areas such as transcription analysis, protein interaction analysis, data mining and text mining.A Java-based tool, for visualizing protein-protein interactions.A software Framework for compiling biological interactions and analyzing networksThe Osprey Network Visualization System is a tool for visualization and manipulation of complex interaction networks.The basic idea of Arena3D is to use multilayered graphs to visualize biological networks. In such a way heterogeneous data will be distinguished between each other.Reactome is a free, open-source, curated and peer reviewed pathway database. The goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge.KEGG is a database resource for understanding high-level functions and utilities of the biological system. It is a computer representation of the biological system, consisting of molecular building blocks of genes and proteins (genomic information) and chemical substances (chemical information) that are integrated with the knowledge on molecular wiring diagrams of interaction, reaction and relation networks (systems information).The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.Biomolecular interactions and cellular processes assembled into authoritative human signaling pathways3D-partner is a fast web tool to predict interacting partners and binding models of a query protein sequence through structure complexes and a knowledge-based scoring function.A database of protein-protein interactions mediated by interchain ß-sheet formationHPID allows the user to use the protein IDs in ENSEMBL, HPRD and UniProt/Swiss-Prot ID to search protein interactions of interest.The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide.An Information Portal to Biological Macromolecular StructuresBioCyc is a collection of 3530 Pathway/Genome Databases (PGDBs), with tools for understanding their data.SIMAP is a database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes. A database of known and predicted protein domain (domain-domain) interactions.PSIbase is a molecular interaction database. Focuses on the Human cDNA.BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. BindingDB contains 1,039,234 binding data, for 6,795 protein targets and 442,444 small molecules.The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions.Online Predicted Human Interaction Database (OPHID) is a web-based database of predicted interactions between human proteins.PIPs is a database of predicted human protein-protein interactions. The predictions have been made using a naïve Bayesian classifier to calculate a Score of interaction. There are 37606 interactions with a Score ≥1 indicating that the interaction is more likely to occur than not to occur. The Biomolecular Interaction Network Database (BIND) is designed to capture protein function, defined at the molecular level as the set of other molecules with which a protein interacts or reacts along with the molecular outcome.
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data. HPRD has been created using an object oriented database in Zope, an open source web application server, that provides versatility in query functions and allows data to be displayed dynamically.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. NatalieQ is a joint project between the Centrum Wiskunde & Informatica (CWI) and the Centre for Integrative Bioinformatics VU (IBIVU).
Additional InformationThe full MINT dataset is available on the page and can be downloaded in several formats: PSI-MITAB 2.6, MINT flat file, and PSI-MI XML 2.5.
Since September 2013 MINT relies on the infrastructure of IntAct to minimize duplicated effort. MINT now focuses on protein interaction information curated by IMEx databases and SIGNOR a database of logic relationships between human proteins.
It is possible to immediately show the result page of a search by manipulating the url with its parameters. More details can be found in the 'Contacts/Links/Linking' tab.
The current index is version 3.2.112 and searches 42,599 publications for 741,528 raw protein and genetic interactions from major model organism species. All interaction data are freely provided through the search index and available via download in a wide variety of standardized formats.mentha: a resource for browsing integrated protein-interaction networks, Nature Methods 10, 690 (2013). doi:10.1038/nmeth.2561
Atanas Kamburov, Konstantin Pentchev, Hanna Galicka, Christoph Wierling, Hans Lehrach, Ralf Herwig (2011)
ConsensusPathDB: toward a more complete picture of cell biology.
Nucleic Acids Research 39(Database issue):D712-717.

Atanas Kamburov, Christoph Wierling, Hans Lehrach, Ralf Herwig (2009)
ConsensusPathDB--a database for integrating human functional interaction networks.
Nucleic Acids Research 37(Database issue):D623-D628.
The analytical and integrative effort done in APID provides an open access frame where all known experimentally validated protein-protein interactions (BIND, BioGRID, DIP, HPRD, IntAct and MINT) are unified in a unique web application. Creators: Bioinformatics and Functional Genomics Research Group Cancer Research Center (CIC-IBMCC, CSIC/USAL) Campus Miguel de Unamuno, Spain. Export possible. Visualization in separate windows as Java Applet. Additional Standalone Installer APID2NET avaiable that is compatible to Cytoscape. The resultant tool provides an attractive view of complex, fully interactive networks with components that allow the querying, filtering and manipulation of the visible subset. Moreover, as a web resource, PINV simplifies sharing and publishing, activities which are vital in today’s Used to be cPATH.
Pathway information is collected from public pathway databases. All data is freely available, under the license terms of each contributing database. Data can be imported with the BioPAX (Biological Pathway Exchange) format: http://biopax.org/
Offeres a variety of tools: Simple visualizations with PCViz to see genes in pathway context; Advanced with ChiBE and an analyzation tool for pathway relationships (CyPath2).
Tools for computational biologists and software developers are offered as well.
PathBlast is general strategy for aligning two protein interaction networks to elucidate their conserved pathways. This method identifies pairs of interaction paths, drawn from the networks of different species or from different processes within a species, where proteins at equivalent path positions share strong sequence homology.No exact research because it is no PPI VisualizationRuns as Online Java Applet, Java Web Application or Java Local Application. Here we do reasearch on web applications so just number one and two are focused. As Java Applet, an addtional windows opens up and shows a visualization with several features. By define, this sort of applet would not be analyzed by this paper in detail.Berger SI, Iyengar R, and Ma'ayan A. AVIS: AJAX Viewer of Interactive Signaling Networks. Bioinformatics 2007 Sept 12; pmid:17855420.The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.Tool can be downloaded (Windows, Mac, Universal JAR) or launched (32/64 Bit) using Java-Web-Start (.jnlp File).
Tutorial and introductory videos are available.
Redirects to new Interface: http://visant.bu.edu/Visualization Tool needs to be downloaded and installed. Visualization Tool needs to be downloaded and installed. - not online availableSince the application is offered as an applet it is possible to integrade it as a Web-Tool. It is free of charge since it is distributed under the Gnu Public License.Registrations required for Downloading the Application.
E-Mail address does not need to be confirmed before downloading.
Various import & export formats are available
Freely available for academic research only.
Terrible Web-Page design.
Registration required for downloading the application; does not work properly. "CGIWrap Error: User not found" thrown upon registration.
Allows importing datasets from a tool called CUPID (Curator of Pivot Interactions Datasets).
Works for four different species: human, yeast, drosophila and mouse.
Used to be: PIANA
Installation only from Source-Code.
Can be used as a Cytoscape Plugin.
Has no visualization features itself.
Is mainly used for parsing external entities (genes, proteins, interactions).
Download Links do not work.
The Link to the original Page (http://biodata.mshri.on.ca/osprey/servlet/Index) does work but the page does not produce and content. "An Error Has Occurred appears at all times".
Arena3D are currently working on a Java-Web-Launch application. A .jnlp file can be downloaded which does not work (yet), the following is mentioned on the download page: "currently not available, we're working on it". Source Code and sample files are available as well.

"Mouse with 3 buttons is also required for easier navigation: left button is used rotation, middle button for zooming, right button for shifting."

Free for academic use.

Several additional libraries are necessary for installation.
Has visualization features. The focus is on pathway analysis, not on protein-protein interactions; therefore we will not analyze it in detail. It is supported that Protein-Protein data from external databases can be overlayed onto the pathways. See [1] for more information.

A Human PPI dataset (in Tab-delimited and PSI-MITAB format) can be downloaded as well as a full list of PPI, including non-humans.

[1] http://wiki.reactome.org/index.php/Usersguide#Molecular_Interaction_Overlay
No Protein-Protein interactions, focuses mainly on Genomes.
The Protein knowledgebase, consists of two sections:
Swiss-Prot, which is manually annotated and reviewed.
TrEMBL, which is automatically annotated and is not reviewed.

About 98 % of the protein sequences provided by UniProtKB are derived from the translation of the coding sequences (CDS) which have been submitted to the public nucleic acid databases, the EMBL-Bank/GenBank/DDBJ databases (INSDC)

New UniProt webpage: http://beta.uniprot.org/
Provides Databases, Downloads, Submissions, and Tools for proteins, genomes DNA/RNA etc.

A List of protein Databases can be found here:

A List of protein Tools can be found here:

Seems to have no protein-protein interactions or visualizatons.
Focuses on pathways3D-partner first utilizes IMPALA to identify homologous structures (templates) of this query from a two-chain complex profile library. The interacting-partner sequences of these templates are then used to search interacting candidates from protein sequence databases (e.g. SwissProt) by PSI-BLAST.Is rather small. Users can create queries and specify them with several attributes.References HPRD.
Page is supposedly best viewed with Internet Explorer 5.0 or higher and netscape 7.2.

The "Visualization" tab can only be accessed when on a Windows system.
A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. "5739 results match MDM2"If you create an account you can see your previous modellings. You do not have to create an account to use the modelling tool.PDBe, PDBj, and RCSB are the member organisations of PDB.

Has its own app for iPhone/Android called "RCSB PDB Mobile"
"BioCyc provides tools for navigating, visualizing, and analyzing the underlying databases, and for analyzing omics data:"
There are broken Links on the site. A video Tutorual "A Site overview --> Intro" helps the user to find his way.
Databases are devided into Tier 1-3, based on the quality.
Search spaces can be defined (programmatically), meaning: you can choose which DB's you want to look through (at the bottom):
"DOMINE is a database of known and predicted protein domain (domain-domain) interactions."

DDI vs PPI ?! Difference where?!
Here: http://www.ncbi.nlm.nih.gov/pubmed/12368246

I don't think we need this one since I have never seen any of the databases mentioned
It focuses on structural interaction of proteins and their domains. It is based on PSIMAP that is a map of protein interactome. It covers the interaction of all known 3D protein structures. Presently, PSIMAP is based on PDB and SCOP databases. It is also the first protocol that has mapped large-scale structural interactions and that used protein families."comprehensively study protein-protein interactions between large KIAAproteins"

Seems rather small (see list of interactions)
Offers Video Tutorials
Users can contribute data, which will be checked and the made publicy available if proven correct.
404 - Page not foundfree to use as long as cited appropriatelyThe resource links to many other databases. Our search queries did not return any interaction data.archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records.Notes: Supporting the visualization of protein interaction networks. Commercial entitties may not use this site without prior licensing authorization. Academic use free if appr. cited.
Notes: Query for visualization not based on a single protein but on a network. - Therefore not part of the detaillled comparison study.
Supporting multi platformRuns in a browser with java. Requirements are Java Version > 2 and an actual browser: So yes, it supports multi platform. If the user wants to inspect the graph in detail, he has to download an additional tool called NAViGaTOR.The graph visualization runs with Flash. So there is just the Flash plugin necessary. Runs in a browser with java. Requirements are Java Version > 2 and an actual browser: So yes, it supports multi platformThe graph visualization runs with Flash. So there is just the Flash plugin necessary. No special software requiredThe graph visualization runs with Flash. So there is just the Flash plugin necessary. Mentha`s so called "interactome browser" comes with Java. A newer but also limited SVG versionis also provided as alterantive to Java. Dynamic rendering of SVG visualization in all modern browsers.As Java Applet multi platform ready but Java Version may be outdated sometime.Yes, however best viewed in Chrome Browser.Yes, the PCViz visualization supports web visualization without installing any 3rd party viewer. Only a browser is needed.Runs in browserYes: Java Web ApplicationDIP is available as a *.jar package. But Java alone is not enough to start the program. An additional package/software is needed, called "Cytoscape". Cytoscape requires Java 6 or 7. Older or newer versions are not supported. So this application gets some minus points in multi platform support. This network visualization tool is available as installer for mac, windows and linux or as archive supporting the same operating systems. Java required.
Available for OS X, Windows, and Linux.
Java required.
Available for OS X, Windows, and Linux
Java required.
Available for OS X, Windows, Linux, and Unix.
Java required.Available for Windows (.exe) and all Unix based Operating Systems (.tar.gz).
~ 180 MB Suite/Archive.
Java required.Cytoscape required if BIANA is going to be used as a plugin.
Requires Python and MySQL Server under OS X.
Java required.Standalone Java Application.
Desktop Applications run on OS X, Windows, and Linux.
Applications are (all Java):

KegHier - For browsing BRITE hierarchy files
KegArray - For microarray data analysis
KegDraw - For drawing compound and glycan structures
No, only on Windows accessibleiHOP provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research.
Usability in generalIt is very hard to do a search. To do a search query for a protein, the user has to select protein search first. After that there are three preselection radio buttons, to define in which format the name is provided. Here it would be better to do a search in all subsections and let the user choose after the search gives some results. It is very frustrating to enter the searched protein every and every time. Searching is very easy. There is no preselection necessary, so the user can just type in the search query and gets a huge result set with many subcategories.The view is clear and easy to understand. The 'Search' Tab is located next to 'Home', which shows that is is the main purpose of the page. On the search page one can also search for publications. The search for proteins can be done by providing the protein/gene name, accession number, or key words. One can also select either all organisms or one specifically (but not multiple since it is handled by radio buttons). A list of the results is provided where each result can be viewed in detail by clicking the '+' (which should -- but doesn't -- change into a '-' afterwards). By selecting one of the results the page changes into a new view: The details of the selected gene are provided on the left wehreas the 'partners' are listed on the right.
In order to start the visualization, an exception in the security settings has to be added to trust the page.
The layout is held quite simple, and small. The user can't miss the search field. Search by protein name is the default whereas the organism can be auto-detected. The list of organisms is tremendous. A search by protein sequence, multiple names, and multiple sequences is possible as well. The buttons below the search field need getting used to and look a little outdated. Eventhough the database is immense, the search is fast. and lists the results properly, highlighting the search term in the 'protein' column, listing the organism in the first column and auto-selecting the top most organism. The back/continue buttons are located at the top, indicating that this page is only a pass-through to gather further information from the user.
Once the user continues, the detailed results are shown, simple and quick.
The search function is emphasized on the home page and very straight forward. On the side the user can select either search by gene (default) or search by Publication. By default all organisms are being searched, the user can restrict it to one organism if (s)he wants to. Furthermore, an advanced search, search tips, and featured datasets are provided. At first sight the page looks a bit overwhelming since it contains a lot of text, but one gets familiar with the layout rather quickly.
The search results are structured nicely, only results which include interactions are shown but the user can expand the list to show all results. The organism for each result is right-aligned within the area of each result which is highlighted with a light blue background.
Only very little information about the proteins is shown at this step, to get further information the user has to select one of the results which results in a detailed view. This detail-view is split up into an area for information about gene ontology, statistics, and interactions.
The graphical viewer can be found in the 'statistics' section, not that easy to find. It is labeled with 'Visualize Interactions Graphically'.
The usability is genrally quite good although it takes some time to get used to the layout of each page since at most of the pages a lot of information is provided at once to the user.
Steps were taken to collapse lists and only show them if the user selects them which is a big plus, since without these simplifications the usability would be a catastrophy.
The page itself has quite a substantial load time, probably due to the bad infrastructure (latency wise) in Portugal since UniHI, as well as the IP address the web page is running on, is loacted in Faro, Portugal. Consequently, every request to the page takes quite some time, often even a couple of seconds to complete.
The page is held simple with a tab bar at the top which is not implemented too well since it waggles around if you mouse over one of the tabs. The 'Search' tab is the starting point of the web page. An organism has to be chosen for a search which is 'human' by default. An example query is entered into the search field which needs to be selected and removed, a clear button is provided to make it easier. Multiple genes or proteins can be queried at once using the common delimiters.
The 'Submit' button starts the search and redirects the user to the results page which includes a tab bar with 4 tabs: Proteins, Physical Interactions, Regulatory Interactions, and Network. When selecting one of the tabs, it is hard to figure out if the page recognized the request since no change in color appears and the page does not react at all due to the long response times.
The results of the search can be checked manually or with (Un-)Check All buttons. Synonyms and several differend IDs (EntGID, UID, NGID, EnsGID, etc.) of the results alongside of KEGG Pathways are presented to the user. Furthermore buttons with links to several databases are available as well which open at the result pages of the specified database, using the query from the users search.
APID search allows for several input names (schema as well as alternatives). The search results are presented in a concise way. By clicking on the number of interactions you get a more detailed overview of the interactions with the protein searched for, also including the number of experiments and information about provenance of the various interactions. By clicking on the "graph" labelled button the java applets is loaded into a separate window.js based web page, a little bit slow. start with selecting context and then provides starting with empty canvas or search for protein and/or other rules.The web page is held very simple and clear. The search field is the center of attention and is labeled with 'Start exploring'. Several tools are available for download a little further down. The web based tool is called PCViz and can either be started by clicking the 'Start exploring' button, which includes a search for BRCA1, BRCA2, MDM2 by default, or by selecting PCViz in the 'For biologists' category which starts the visualization with one random sample.
Due to the simple layout, it is clear that the visualization is the focus of the page.
Needs two proteins at minimum as input to identify pairs of interaction paths therefore not explicitely suitable for exploring the interaction of one protein
Interoperability (Import, Export, Formats, Plugins)In the web-view, there is just one option to export the graph to NAViGaTOR. The graph view data is not exportable but the protein data itself is. The user can open the current network to Cytoscape to do more complex research.Not providedSave of network is provided in several file formats. png, svg, txt, xml, dat, faThe visualized graph is not able to be exported.Export to Text File (txt), Image (PNG), and PDFThe new version does not provide export or import. The java version supports export as textual tabular data and png graphic.Load data is possible. saving graphic (png, svg) and table (csv) view can be saved too. sharing via URL.Import via BioPAX. Export as png, sif or BioPAX. Embed the visualization control via iframe.Because there is a standalone application for the visualization, the interaperability is excellent. The user is able to import, export and store the created network and share it with other researchers.
Visualization (Speed, clarity, usability)The web-view is very waggly, this means the displayed nodes and edges are shaking constantly which is very disturbing. The speed of this visualization is quite good. It was tested with approximately 100 nodes and 100 edges. Everything moved quickly and in a smooth way. Even the unfixed nodes followed the "owner" without any delay. On the right side there is a short description of all features and how to use the viewer in a correct way. A good feature is to fix single nodes while others stay unfixed. This improves the usability enormously. The fixed nodes can be selected by hitting a button in an overall menue. This menue provides a huge amount of different interaction features for the user. Selection of the node can be done in a single way by clicking with the left mouse button or drawing a selection area with left mouse button pressed. To improve the selection feature and make it easier to do special selection scenarios an inverted selection feature is provided. Select or deselect all and a full tree selection of the corresponding node is also possible. Even selection by pathlength is supported where all nodes within a length of n edges starting from the currently selected node will be selected. To enhance the visualization clarity the node labels can be toggled and the shape of the nodes can be switched between circle, square, diamond and triangle.Speed is fast and it is really easy to use. Thats because there are just a few features supported by the viewer. For lightweight research this could be enough but for complex interactions this will be hard to understand. A pro is that when a node gets selected by a left mouse click, the name of the protein pops up over the node itself. As long as the user keep the left mouse button pressen, he/she can read the name. A helping selection feature is "select first neighbour". This selects the first node connected to the currently right clicked node.If there are more than one, all nodes get selected. The CytoscapeWeb Controls on the right side of the visualization was not working when the visualization was tested. On the test system it runs smoothly, when working with less than 50 nodes. Additionally, the user can change the node size to improve speed and clarity. A threshold can be selected, to get just the nodes with a specific connection rank. The nodes can be drag-and-drop to improve current view. To support this feature, the view can be frozen (otherwise the nodes just follow the one which is being dragged) and un-frozen. With 'UnFreeze' enabled, some nodes are waggly. This is annoying and should be prevented by some mechanism. The three options: 'expand', 'protein size', and 'score threshold' as well as the sliders which go alongside are not well displayed, they are too small and inconspicuous compared to the buttons below.
The view is split in two areas. On the right side the viewer itself is placed and on the left side, the user can find the detailed view of the node, which is currently selected in the viewer. Additional attributes about the current protein like name, deseases, reactors, interactors, or which organism this protein is assigned to can be found in that section.
Server response time is generally good enough to work continuously without longer periods of waiting time unless the user wants to use the 'connect' feature on a newly selected node, which adds edges from this node to the ones it is connected to in that graph. This takes a lot of time. The MITAB and PSI 2.5 button also take a lot of time and there is no indication provided for the user that the server is working on the request.
The visualization is at the top of the result page and looks rather simple in the beginning since STRING decided to only show couple of nodes. The user can increase them by hitting the 'more' button below, the 'less' button does the opposite. The user can also change the view of the visualization (confidence, evidence, actions). Above the visualization he can change the layout by 'relaxing' it, apply clustering mechanisms (Kmeans, MCL), perform enrichments, and several other options like Background image, hiding protein names, and adding/removing nodes. Everything works smoothly and is quick. The user can adjust the level of clarity himself, as it starts out very simple and clear and not overwhelming like many other visualizations.
Adding new proteins is possible with a single left click, additional information gets displayed in a pop-up. A static or dynamic mode is available. Furthermore the visualization is not limited to the graph view. Other views are: neighborhood, fusion, occurence, coexpression, experiments, database and textmining. Interactions can be limited to any amount and the score can be limited too. Displaying additional white nodes is also supported. The usability seems endless.
The visualization takes a lot of time to load compared to other visualizations. In the top left corner the number of total interactions is listed. Below are attributes which show the details of either the selected node, or (if no node is selected) details of a node at a mouse-over event. Interactions can be searched (a pop-up seach window appears) and followed. The 'follow' function was only tested for functionality (due to the lack of biological knowledge) and seems to be working. This might be a key feature for biologists.
The user can also apply a filter on the throughput (Any, High, Low) and on interactions by (un-)checking tiny check boxes. The size of those is definitely too small.
To the right is a list of check boxes as well which corresponds to the nodes. The categories of the nodes are 'Physical' and 'Genetic' sub-categories depending on the proteins. Removing nodes/edges in a large, well-connected graph takes quite some time since the visualization semms to be built up from scratch again. Speed can definitely be optimized, but is not too much of a burdon, considering the testing environment with 200-300 nodes.
The visualization is based on a circular layout and no other layout options are available. With many nodes and edges, this results in a chaos in terms of clarity. Since the visualization is static and the names of the proteins are placed around the circle, some of them are even up-side-down. Therefore, looking for a specific protein can be quite challenging although the proteins are listed alphabetically.
Edges are not clickable. When selecting a node, edges connected to this node are highlighted and the size of the font of the partner proteins increases, overlapping with its neighbors making it hard to read.
In terms of usability, the base is not too bad but a lot of improvement in terms of readability and adjusting the visualization to the users needs can still be done.
The visualization can be found in the 'Network' tab of the result page. The build up takes quite some time (about 150 nodes), renting a server with a better connection would probably improve it substantially. Moving nodes around works smoothly as well as selecting multiple nodes by area-selection. In the visualization there is no detailed information available about the nodes, the user has to use the tabs 'Physical Interactions' and 'Regulatory Interactions' where tables are provided and can be downloaded (txt). When selecting an edge, a pop-up window provides details about the interacting partners. Connections of different types are colored differently in the visualization (red and blue).
The visualization has many filter and analysis options which are situated to the right of the graph. The default category is 'Filtering of Molecular interactions', which can be filtered by: Connecticity, Resource, Method of Derivation, Scale of Experiment, Minimum Number of PubMed References, and Type of Interaction. To apply a filter, the 'Update Nodes' button needs to be pressed which again takes quite some loading time.
Furhter categories are: Filter and mapping of gene expression from DB, Filter and mapping of own gene expression data, Filter and mapping of Drug targets, Enrichment Analysis, Enriched Datasets and Phenotype Analysis, Map Your Genes, and Regulatory Interactions. A link to the 'Help' page is provided within every category to explain in detail what it does and how it can be used.
A reset button is provided to recunstruct the original graph setup.
The dynamic network viewer features zoom, filter and details on demand and provides a flexible layout. Moreover, the java version offers possibilities for coloring and highlighting.APinBrowser comes with zoom and filter and provides limited details on demand. Minor coloring possibilities such as background color and adjusting edge thickness do not fill the gap of missing features such as highlighting certain nodes and edges, visual clustering etc.The default layout is simpley called network. PINV also provides a circular layout, heatmap, and table.The speed is good, but not as good as some other visualizations. This could be the disadvantage of not using java or other technologies. The viewer is written in Javascript and uses some Cytoscape libraries. Usability is good enough for simple visualizations, for doing deeper research the export functionality is probably the better way to go since it can then be analyzed in BioPAX or other PPI visualization tools supporting the provided formats.
It's easy to add more proteins to the visualization by simply clicking on a plus button in the search bar. A relation between two ore more proteins of interest can be displayed in that manner. When selecting a node in the graph, the details are shown to the right of the viewer, providing the user with a short description which can be expanded, Aliases, another Description, Chromosome Location, UniProt ID, and Gene ID. Edges can be selected as well, information details then include Co-citations, Interaction Type, and References. A 'Download'-button for the detailed process (for BioPAX) is then provided below.
In the 'Settings' tab the user can select the interaction types (edges) and can hide/show them by clicking on them. The number of genes can be adjusted by a slider below as well as the Query type which is either 'Neighborhood', or 'Paths-between'.
The user can reset the graph and show it in Full screen mode as well.
The graph itself is fixed, nodes only move around if the user moves them. To select a node the user has to click on it, area-selection is not possible.
An additional feature in this database is, that the user can load cancer context to see the overall frequency of alteration for each gene in the network.
The speed is excellent for small networks. On the one hand, this is a benefit of standalone application against browser visualizations. On the other hand, this could be because the technique is so much better. Some more research has to be done here, to make a good explanation.
Visualization featureszoom, drag and drop, drag workspace, occupacy, select, area-selection, select inverse, delete nodes, delete edges, show/hide labels, toggle shape, scale, rotate, fix/unfix, layout using forces, randomize, centre, circularize, linearize, spread neighbours, adjust force, pan, search and display, display tooltips, frame, select all, deselect all, shrink selection, grow selection, select fixed, select hubs, select by pathlength, select treelabels, area-selection, drag and drop, drag workspace, zoom, fit to screen, select first neighbours, expand network around this moleculedrag and drop, expand, protein resize, score threshold, freeze, unfreeze, connect, score, MITAB, PSI2.5toggle between confidence-, evidence-, and actions view, fix, unfix, clustering (KMEANS, MCL), enrichment, add more proteins, delete proteins, view additional data on clickmany filter options, details on mouse-over, show connected partners, search/follow interactions, download interactions.txtZoom, Drag and Drop, drag workspace, area-selection, Reset, Fit to Screen, several filter optionsNetwork viewer, zoom, filter, details on demandzoom, filter, limited details on demandzoom, highlighting and filter by applying rules on various ways to the search - starting with an empty canvas possible. Some hover effects and details on click but no further exploration interactivity. Exploration is mailny done by applying rules.
Zoom, Drag and Drop, drag workspace, zoom to fit, Gene threshold, show/hide edges of specific type, Full screen, Reset
Rotate, Translate, Zoom In/Out, Centre View/Rotation, Select Single Node, Select Group of Nodes, Select More Nodes, View Selected Nodes, Move Selected Nodes
Visualization static or dynamicdynamicdynamicdynamicdynamic and staticstaticdynamicdynamicdynamicdynamicdynamicn/adynamic
Flexibility, minimal drawing area, maximal symmetryDrawing area resizableAutomatic resize when additional nodes are added. pure static view with on hover on effectnoyesyesyes
full screen mode provided
3D Layout quality criteria: Transparency, Depth, PerspectiveNo 3D supportedNo 3D supported3D isn't supported3D isn't supportedNo 3D viewNo 3D viewnonononoNo 3D view
GUI (Qualitative description of graphrical user interface: The GUI should allow users to customize the vis. by changing look and feel; adding annotations)Visualization is not customizeable (besides the change of the node representation), No annotationsNo annotationsJust check boxes to toggle visibility of interactions, and specific protein nodescolor palette, customizableapplet menu provides basic features such as backgroudn coloringFilter and higlight with color by defiing rules and uploading expression data possible
Collection of analysis instruments (extract information from the graph without external tools)It is possible in a very basic way.no analysis instrumentsEnrichment Analysis, Enriched Dataset and Phenotype Analysisminimal menu functionshardly any graph overall methods ... limited spatial cluster possibilities, adding manipulation rules (from BIOJS), getting attributes like closenees for each node by clicking on it
Number of links to different PPI sources292766~23121563218> 4 (not all sources are provided on the homepage)710 (uses only its own data)~20 (not all of those listed below are DB's, there are some tools in there as well)615120 (uses only its own data)0 (uses only its own data)1
User account supportedNoNoNoNoYesNoNononononoNononoYESNo
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Total amount of PPI1,539,758447,368330,377compare Mint332,235,675543666 (787370raw)374,833
467364 (158485 human)
183,678322579 (83670 human)2942636 (human)n/an/a1,317,041
Evidence based - / Source PPI635,488n/a323,595compare Mintn/an/an/an/an/a44,040n/an/an/a1,016,751
Predicted PPI922,617n/a6,782compare Mintn/an/an/an/an/a278,539n/an/an/a300,290
Search result interactions for MDM2 (UniProt: Q00987)351536 (6407 in other databases)56 (6681 in other databases)56 (6681 in other databases)n/a302378n/a1510670
Search result interactions for VDAC (UniProt: P21796)8762 (611 in other databases)2 (6951 in other databases)2 (6951 in other databases)n/a587n/a0
PPI Databases usedBioGrid, BIND, DIP, IntAct, MINT, Fawcett, Chen, INNATEDB, MGI, WandEScmplx, NON_CORE, TewariTGFb, Krogran, Yeast, AGRAVAL_MYC, BCI, Blagoev, HPRD, I2D, Miller, Jones, Moran, Nakahira, Pawson, ShawnLi, SOURAV_MAPK, Stelz, Vidal, WranaAPID, BioGRID, bhf-ucl, ChEMBL, DIP, HPIDb, InnateDB, IntAct, mentha, MPIDB, MatrixDB, MINT, Reactome, Reactome-FIs, STRING, BIND, Interoporc, I2D-IMEx, InnateDB-IMEx, MolCon, UniProt, MBInfo, BindingDB, VirHostNet, Spike, GeneMANIA, BARDIP, Intact, MPact, PPID, BioGRID, Human protein reference databaseDIP, Intact, MPact, PPID, BioGRID, Human protein reference databaseCOG, Ensembl, Intact, RefSeq, PubMed, Reactome, DIP, BioGRID, MINT, KEGG, SGD, FlyBase, SwissProt/UniProt, SwissModel, HUGO, OMIM, NCI/Nature PID, PDB, The Interactive Fly, BioCyc, Gene Ontology, SIMAPEnsembl, HGNC, HPRD, VEGA, OMIM, Entrez Gene, RefSEQ, GenBank, UniprotKB (but cooperates with more Interaction Database Partners such as
Molecular Interaction Database, Intact Interaction Database, Database of Interacting Proteins, Pathway Commons, International Molecular Exchange Consortium, iRefIndex , STRING etc.)
MDC, CCSB-Y2H, HPRD-BIN, HPRD-COMP, BioGRID, IntAct, DIP, BIND, REACTOME, COCIT, HomoMINT, OPHID, TRANSFAC, miRTarBase, HTRIdb(Imex), Mint, Intact, DIP, MatrixDB, BioGridprobably all important ones: BIND, BioCarta, Biogrid, CORUM, Chembl, DIP, DrugBank, EHMN, HPRD, HumanCyc, INOH, InnateDB, IntAct, KEGG, MINT, MIPS-MPPI, MatrixDB, NetPath, PDB, PDZBase, PID, PIG, PINdb, PharmGKB, PhosphoPOINT, PhosphoSitePlus, Reactome, SMPDB, Signalink, Spike, TTD, Wikipathways, => ConsensusPathDBBioGrid, BIND, DIP, HPRD, IntAct, MINT, UniProt, iPfamI2D as common large database for providing example data sets but recommends using own data as wellHPRD, Reactome, NCI_Nature, PhosphoSitePlus, HumanCyc, biocyc, PANTHER Pathway, pantherdb
probably outdated
MIPS, BIND, HPRD, BioGRIDProsite, InterPro, Pfam, PRINTS or SMART search is supported directly on the page??? Not providedDIP, IntAct, STRING, MINT, BioGrid
Protein Data Bank (PDB)
AstexViewer, BLAST, CDHIT, DeepView, DFIRE, DINO, DSSP, Disopred, Gromos, HHblits, HHsearch, IPRscan, Jmol, Matplotlib, MEMSTAT, Modeller, Molscript, NR, PDB, PDBsum, PQS, Procheck, ProMod-II, Promotif, PsiPred, QMEAN, InterPro, Rasmol, Raster3D, SSpro / ACCpro, UniProt, WhatcheckEcoCyc, MetaCyc, Humancyc, AraCyc, YeastCyc, LeishCyciPfam, 3did, ME, RCDP, P-value, Interdom, DPEA, PE, GPE, DIPD, RDFF, K-GIDDI, Insite, DomainGA, DIMAPDB, SCOP, SWISS-PROT, InterPro, ProDom, Pfam, PRINTS, PROSITE, SMART, TIGRFAMs, PIR, MGDSWISS-PROT
Access Frequency, Maintenance NotesEBI is supporting this tool, therefore quite uptodateUniroma created and provides this tool. Uniroma also provides MENTHA, which already integrates some newer visualization tools, not only limited to Java.same as mint~4780755 per month
... developed at CPR, EMBL, SIB, KU, TUD and UZH, therefore very uptodate (has big institutional and financial supporters)
Princeton, NIH are not the biggest financial supporters, but they have many other partners tooDevelopers are CBME and other not so big players but makes use of the most important and comprehensive databasesonly small institution but makes use of many big databases and manual upload toohardly no updates done to visualization since the last years due to small institution supportersn/an/a
Usability remarks search tool- Search does not provide any autossugest and correction suggestions. If you search you have to search precisely. Other tools already provide such features. - search results table very limited too, only links to other metainformation on other platforms and no filter and sort possibilities, though it woul be essential to know which interaction has which type at first sight.search sometimes quite slow, has limited possibilities for advanced search. search results are presented in a summary table with useful additional information on the interactionssearch provides also results from other databases but divides its' presentationsame as mintSearch includes many other databases about multiple organisms.simple search offering quick glance at search results, also filter- and sortablefirst search results are linked to other tools. Right next to proteins information tab we find the list of interactions.. Result table is not sortable/filterable but downloadable. Additional information is providedintuitive search field, possibly more strange presentation of the results. Browse-Button starts graph view. List button shows interactions and a lot of interestringly presented meta information.intuitive search, quick results, mapping criteria for filteringSearch is straightforwardsee aboveConnection problems during review phase. pathbalst was down for some weeks.
Usability remarks visualization tooljava security setting is a manko too. - visualization is interactions are not intuitive - the combination of control menu and buttons is quite hard to understand. visualization possibilities are limited and outdated, no antialiasing ... errors in graph viewer are not supportive, only the export possibilities and the textual table is usefulflash graph is useful and supports the sense making process, export possibilities to cytoscape is useful tool as well as the switching between the list tab and the graph tab. However, interesting possibilities such as filterint sepcific types of interactions, additional information on nodes and on the graph edges are not integrated.mint viewer is based on java and therefore not fully up2date, however it offers interaction possibilities, zoom and filter and additional information. A graphical legend is missing for a quick glance what means which color and shape etc.same as mintNext to several dynamically rendered PNG Graphs it is also possible to use an interactive flash visualization tool with many filter and control features as well as visualization adaptations such node/label hide/show but also more functional ones like clustering, enrichment etc. Also export possibilities of graph are provided. Furthermore, next to the network summary views there are also other possibilities for simples visualizations such as the occurence view. If available, additional information as well as structure graphics are included an can be shown within the context menus of the several nodes by clicking on it.Graphical viewer is a little bit hidden, but if found, it loads quickly. The view does not require any plugin and makes use of a modern radial layout. interaction possibilities include amongst other highlighting, searching and filtering. The radial view is not so much intuitive as traditional graph renderings and the small labels are hard to read. However, additional information is found quickly during the exploration process. Remark: Color and shape would rather enhance the visualization.Though flash is used the visualization itsellf is presented in an old fashion manner and quite similar to the viewer of Intact. SImple yet fast and interactive it provides a quick glance at additional information. Interactive features include view manipulations such as zooming, filtering, node movement etc.Java and newer not Java Visualization possibilities are provided. Alternative version is intuitive but still limited, but may be update din near future. Zoom, Filter through treshold in the newer one and many others within the java version. The visualization itselft therefore supports the sense-making processnot so fancy, not so good overview but provides many possibilities and includes many information sources. Usability is not a good one, you have to do much manual search work.The graph (named APIN) comes as java applet in an quite old fashioned manner without antialiasing. however it supports zoom, search and filter. Interactivity is quite limited, edges and nodes are highlighted on mosueover, the graph is movable on click on the nodes, and click on edges allows displaying detailled information on the interaction itself. see also abovesee also above
# Binary Interactions for Search after GASP1 (Q5JY77): for homo sapiens/human5323 using search term "GPRASP1" 22 using UniprotID1717depending on confidence score, default is limited to showing 10 interactions at max for a medium level of confidence score (of 0 400) ... with the same score are 37 results found if not limited to 10, and at a conf. score of 0 150 there 201 interactions found355035149 interactions (60 distinct ones) 5295n/a - does not show protein protein interactions but details about genes and their interactions extracted from multiple pathway data resourcesn/a - needs at least two proteins for input38
# Interactions (individual nodes counted) for Search after human GPRASP1 (Q5JY77), cannabinoid 1 receptor CNR1 (P21554), calcitonin receptor CALCR (P30988), dopamine D2 receptor D2DR (P14416), bradykinin 1 receptor BDKRB1 (P46663)53 + 5381821 expanded to 9321 expanded to 93internal 2 (confidence score 400) up to 7 (confidence score 150) and external 470 with std. conf. score and 167 with confidence score 0.9n/a284674192911894n/a
# Disease associations using standard search of GPRASP1n/aoption (show more data from EMBL-EBI) results in 2 disease associations using "GPRASP1" but 0 using UniprotID
33primary search associated to 7 (10interactors) to 13 (37 interactors) diseasesn/a0 within KEGG pathway associations0 within KEGG pathway associationsn/an/an/an/a
DB Version Numberversion 2.3IntAct View version: 4.1.42011.08 UniProt API versioncompare MINTversion 9.1Database Statistics Current Build Statistics (3.2.117) - October 2014UniHI version 7.1Last update: 26th October 2014
Release 29 (27.06.2014)
APID Release FEB - 2009 (09-2-09)Version with latest update Oct. 23rd, 2014.latest release Nov 201338706
12/09/2008 Release of v1.1
Release 9 04-13-10 Apr 13, 2010
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