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

BMC Research Notes

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

Input dataset^a	Version^b	The number of protein structures
		Input^c	Output A^d	Output B^e
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-redundant^f	-	4,544	1,172	7,901

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.
^aEach input dataset contains a list of PDB entries of ligand-bound state proteins.
^bThe version of the input dataset or the date when the input dataset was downloaded.
^cThe number of ligand-bound state protein structures in each input dataset.
^dThe number of unique proteins that were paired with at least one ligand-unbound state entry by the BUDDY-system.
^eThe number of total pairs.
^fUnion of all ligand-bound state protein datasets.

ISSN: 1756-0500