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Table 1 Summary of the results obtained using the BUDDY-system against various datasets

From: BUDDY-system: A web site for constructing a dataset of protein pairs between ligand-bound and unbound states

Input dataseta Versionb The number of protein structures
   Inputc Output Ad Output Be
AffinDB [17] 2008-03-17 476 157 2,257
BindingDB [15] 2008-03-17 1,485 484 4,629
PDBbind [18] v2007 3,124 996 7,000
PLD [16] v1.3 485 137 1,277
CCDC/Astex Test Set [8] - 305 91 611
Astex Diverse Set [10] - 85 25 170
Non-redundantf - 4,544 1,172 7,901
  1. This table shows the results obtained from the BUDDY-system when various databases were input as lists of ligand-bound states proteins. Taking BindingDB as an example, when 1,485 PDB entries obtained from BindingDB were input as a ligand-bound state, at least 1 corresponding unbound state PDB entry was found for 484 of 1,485 input entries; a total of 4,629 pairs were obtained.
  2. aEach input dataset contains a list of PDB entries of ligand-bound state proteins.
  3. bThe version of the input dataset or the date when the input dataset was downloaded.
  4. cThe number of ligand-bound state protein structures in each input dataset.
  5. dThe number of unique proteins that were paired with at least one ligand-unbound state entry by the BUDDY-system.
  6. eThe number of total pairs.
  7. fUnion of all ligand-bound state protein datasets.