DIPS-Plus
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question - are all protein pairs direct interactors?
I was thinking of using DIPS-Plus for training a classifier for protein-protein interaction (I confess I have little experience in ML, any advice welcome). The database describes the pairs based on the distance between their atoms, and I saw some few examples of pairs where there are less than 5 atoms within the threshold distance. So two questions:
- are all pairs direct interactors? (eg say we have a PDB with chains A, B, C, where A::B and B::C, but not A::C. Would the pair A::C be included in the database?)
- suggestions to create a set of non-interactors? As a I understand DIPS-Plus you can train a model to tell if any two atoms are interacting or not, but not (as is) to train a model to tell if two proteins are interactors or not.
Perhaps the second question is more for eg Stack Exchange, but I'm open to any advice here!