Protein-protein interaction databases

From OpenWetWare
Name Description Link
GPS-Prot 3stars.png Comprehensive protein-protein interactions; excellent ease of use and completeness, data visualization http://gpsprot.org/
Wiki-Pi 3stars.png A web resource for human protein-protein interactions; excellent search results http://severus.dbmi.pitt.edu/wiki-pi/
String 3stars.png database of experimental and predicted interactions; excellent graphics http://string-db.org/
IntAct 2stars.png derived from literature curation or direct user submissions; tables http://www.ebi.ac.uk/intact/
iHOP 2stars.png = information hyperlinked over proteins; built by literature mining; results as text clippings http://www.ihop-net.org/
BioGRID 2stars.png from literature & high-throughput datasets; best for yeast & A. thaliana http://thebiogrid.org/
MIPS 0stars.png Mammalian Protein-Protein Interaction Database (didn't work when tested in Sept '11) http://mips.helmholtz-muenchen.de/proj/ppi/
Mentha mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way http://mentha.uniroma2.it/index.php
add another database here with description here link

GPS-Prot

  • GPS-Prot allows easy querying and display of human PPIs aggregated from all major databases
  • Includes BioGrid, DIP, IntACT, HPRD, MINT, BIND, MIPS and more
  • Each interaction comes with a link to publications in chronological order on PubMed. Access the entire publication history for any interaction.
  • Experimental techniques curated from the literature are listed for each interaction (e.g. Affinity Chromatography, X-ray crystallography).

Opinion: strong on ease of use and completeness, allows anyone, from students to experts, to view a PPI network easily

Wiki-Pi

  • Wiki-Pi's intuitive search functionality allows you to retrieve and discover interactions effectively
  • interaction is provided with automatically updated annotations of individual proteins from databases such as Gene Ontology, KEGG, REACTOM, Pubmed2ENSEMBL, and DrugBank
  • search for interaction with simple queries such as associations to diseases or pathways, or complex queries conditioned on annotations of one or both proteins in the interaction
  • latest references: [1]

Opinion: great search results, good tabular representation.

String

String-db-logo.gif
String-db-logo-text.gif
  • collects evidence from genomic Context, high-throughput experiments, conserved coexpression, and text mining
  • created by CPR, EMBL, SIB, KU, TUD, and UZH
  • latest references: [2], [3]

Opinion: easy to use, great graphical interaction map, detailed explanation of evidence


IntAct

Intact-logo.png

Opinion: The default is an oversized results table (>2 screen widths on a 13"). Use "Change table presets" to compact. Separate columns for links/alias/pubID could be integrated or hover over to make the default table easier on the eye. Overall, the presentation of results seems to be more geared towards bioinformaticians than users with the table full of codes instead of names (Do you know what 9606 is?). Also, no easy species selection and, more importantly, no graphical overview.


iHOP

Ihop logo.gif

Opinion: All information is presented as highlighted text in sentences which makes the information slower to take in than from a structured table and much slower than from a graphical representation. Hypothetical and possibly indirect interactions (A regulates B), non-existent interactions (A does not bind B), and experimental (A co-precipitates with B) are not differentiated. Easy to use, clean species separation.


BioGRID

BioGRID-logo.png

Opinion: Good interface but generally fewer hits than other databases for mammalian genes. This is probably because this database contains mainly yeast protein interactions where it is very strong. It is currently being extended towards other metazoans. Nice representation of evidence as high & low throughput with reference and description.


See also

On OpenWetWare

  • The Prince lab present on OWW works on protein-protein interactions.
  • OWW's Keating lab also works on protein-protein interactions.

Lists of protein interaction resources:

Related literature searches

  • search PubMed for MeSH term Protein Interaction Mapping [5], major topic [6], and reviews only [7]

Recent reviews:

Wikipedia entry protein interaction, interaction prediction