Is there a well-accepted subset of the Protein Data Bank set of protein structures that:

  1. Has only "high quality" structures (may be differing metrics of this; e.g. resolution, size, or structural completeness)
  2. Has minimal redundancy (e.g. nothing with exact sequence identity from the same species)
  3. Is still as large as possible, spanning as many molecules and species as possible
  4. [Optionally but better] Is not too biased (e.g. certain classes of proteins are highly over-represented in the PDB)

It is possible to download the entire PDB and make up rules for myself, but this seems like something people might have already considered reasonably extensively. I'm hoping for a dataset I can just download and cite, in the best case. :)


1 Answer 1


Richardsons' Lab has a top8000 list. See their paper from 2016.

They also have top500 list, but it hasn't been updated for many years.


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