Question

Protein complex databases - how many are out there?

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7.0 years ago

Qroid ▴ 40

The question is pretty straightforward: what are the published protein complex databases? We typically use CORUM but we're being encouraged to use other databases too, since CORUM is biased to very abundant complexes. A quick Google search shows a few more:

CORUM (http://mips.helmholtz-muenchen.de/corum/)
PCDq (https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-6-S2-S7)
3D complex (http://www.3dcomplex.org/)
IntAct (https://www.ebi.ac.uk/intact/complex/)

Are there others?

protein complex protein interaction database • 5.4k views

ADD COMMENT • link updated 7.0 years ago by Jean-Karim Heriche 27k • written 7.0 years ago by Qroid ▴ 40

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STRING (http://string-db.org)

ADD REPLY • link 7.0 years ago by Andrzej Zielezinski 11k

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Is there an easy way to get complexes from STRING? My understanding is it's just a list of pairwise interaction.

ADD REPLY • link 7.0 years ago by Qroid ▴ 40

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Yes, as far as I know, STRING only has binary interactions.

ADD REPLY • link 7.0 years ago by Jean-Karim Heriche 27k

score 2 · Answer 1 · 2017-05-03

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7.0 years ago

Jean-Karim Heriche 27k

Reactome and BioGRID have some protein complexes. Then there's also FuzDB. The Gene Ontology cellular component domain also has a term 'macromolecular complex' (GO:0032991). However, keep in mind that different resources have different notion of what a complex is and even for the same definition, the granularity may be different i.e. what is one complex in one database may be two or three (sub-)complexes in another.

ADD COMMENT • link 7.0 years ago by Jean-Karim Heriche 27k

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Thanks. Do you have a link to the BioGRID complexes? Again I only see pairwise interactions.