Protein-protein interaction databases

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(database details)
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| http://www.ebi.ac.uk/intact/
| http://www.ebi.ac.uk/intact/
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| [[Protein-protein interaction databases#iHOP|iHOP]]
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| [[Protein-protein interaction databases#iHOP|iHOP]] [[Image:2stars.png]]
| = information hyperlinked over proteins; built by literature mining
| = information hyperlinked over proteins; built by literature mining
| http://www.ihop-net.org/
| http://www.ihop-net.org/
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[[Image:Ihop logo.gif|right|120px]]
[[Image:Ihop logo.gif|right|120px]]
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* genes and proteins converted into hyperlinks between sentences from PubMed & turned into a network
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* genes and proteins converted into hyperlinks between sentences from PubMed & turned into a conceptual network
* originally developed at CNB-CSIC, authors now at CNIO & MIT
* originally developed at CNB-CSIC, authors now at CNIO & MIT
* references: [http://www.nature.com/ng/journal/v36/n7/full/ng0704-664.html Hoffmann & Valencia 2004] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933131/?tool=pubmed Fernández et al. 2007]
* references: [http://www.nature.com/ng/journal/v36/n7/full/ng0704-664.html Hoffmann & Valencia 2004] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933131/?tool=pubmed Fernández et al. 2007]
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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.

Revision as of 05:53, 23 September 2011

Name Description Link
String Image:3stars.png database of experimental and predicted interactions http://string-db.org/
IntAct Image:2stars.png interactions derived from literature curation or direct user submissions http://www.ebi.ac.uk/intact/
iHOP Image:2stars.png = information hyperlinked over proteins; built by literature mining http://www.ihop-net.org/
MIPS Image:0stars.png Mammalian Protein-Protein Interaction Database (didn't work when tested in Sept '11) http://mips.helmholtz-muenchen.de/proj/ppi/
cell 1 cell 2 cell 3
cell 1 cell 2 cell 3

Contents

String

  • collects evidence from genomic Context, high-throughput experiments, conserved coexpression, and text mining
  • created by CPR, EMBL, SIB, KU, TUD, and UZH
  • latest references: [1], [2]

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


IntAct

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

  • genes and proteins converted into hyperlinks between sentences from PubMed & turned into a conceptual network
  • originally developed at CNB-CSIC, authors now at CNIO & MIT
  • references: Hoffmann & Valencia 2004 Fernández et al. 2007

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.


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.

List of protein interaction resources:

Related literature searches

  • search PubMed for MeSH term Protein Interaction Mapping [3], major topic [4], and reviews only [5]

Recent reviews:

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