As stated in the post title,
I am looking for papers/publications with sets of experimentally-validated PPI interactions to be used in a computational biology research project .
Alternatively, what wet-lab techniques/stringent criteria give the most reliable PPI interactions?
Looking forward for your help! Dan
3 answers
As others have suggested, you could use public databases of protein interactions and filtering by experimental support type. However, this can become tricky as some for example consider genetic interaction as experimental support and/or others do not have a clear classification of experimental types. For use as validation set in human, I would suggest to take a look at the Harvard CCSB interactome. They also curated what they call a high quality set of interactions from the public databases.
If you also need a set of protein pairs known not to interact, have a look here.
in the supplementary material of this Science paper (Uncovering disease-disease relationships through the incomplete interactome Jörg Menche et. al, Science, Feb 2015) you can download their human interactome. it includes also PPis
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Two databases you might use: http://string-db.org/
http://mint.bio.uniroma2.it/mint/Welcome.do
(Since you didn't specify which organism I'll be ignorant and assume everyone works on humans. Although those databases are not specific for humans per se.)