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question - are all protein pairs direct interactors?

Open rubenalv opened this issue 7 months ago • 2 comments

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!

rubenalv avatar Jul 02 '24 15:07 rubenalv