The PDBbind database: methodologies and updates.
We have developed the PDBbind database to provide a comprehensive collection of binding affinities for the protein-ligand complexes in the Protein Data Bank (PDB). This paper gives a full description of the latest version, i.e., version 2003, which is an update to our recently reported work. Out of 23 790 entries in the PDB release No.107 (January 2004), 5897 entries were identified as protein-ligand complexes that meet our definition. Experimentally determined binding affinities (K(d), K(i), and IC(50)) for 1622 of these were retrieved from the references associated with these complexes. A total of 900 complexes were selected to form a "refined set", which is of particular value as a standard data set for docking and scoring studies. All of the final data, including binding affinity data, reference citations, and processed structural files, have been incorporated into the PDBbind database accessible on-line at http:// www.pdbbind.org/.
Wang
Renxiao
R
Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, 48109-0934, USA.
Fang
Xueliang
X
Lu
Yipin
Y
Yang
Chao-Yie
CY
Wang
Shaomeng
S
D030562:Databases, Protein; D020407:Internet; D008024:Ligands; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*
D008024:Ligands; D011506:Proteins