The PDBbind Database:  Methodologies and Updates

Abstract

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/.

Consensus virtual screening approaches to predict protein ligands

“…Another approach directed at the re-scoring of predicted binding energies with various ligand-derived chemical parameters, such as the water/butanol partition coeffcient achieved correlation coeffcients of better than 0.9 for individual docking methods (GarciaSosa et al, 2010). However, these studies did not consider decoy ligands, but only the ligands included in the receptor-ligand complex contained in the PDBbind database (Wang et al, 2005). High correlation coefficients between predicted and experimental binding affinities can be meaningless, if they do not lead to a separation between ligand and decoy molecules as shown in this study.…”

The Protein Data Bank archive as an open data resource

“…More than 400 million coordinate sets were downloaded in 2013 from the wwPDB partner sites. Both the utility and the uniformity of PDB data have enabled the development of other databases and datarelated resources, including resources for drug discovery (for a review see [32]); resources focused on small molecules and ligands such as ChEMBL [33], DrugBank [34], BindingDB [35], BindingMOAD [36], and PDBBind [37]; protein structure classification and annotation resources, such as CATH [38,39], SCOP [40][41][42], and PDBsum [43,44]; and focused, specialty annotation resources such as Protein Data Bank of Transmembrane Proteins (PDBTM) [45], ArchDB for functional loops in structures [46], and 3did for protein-protein interaction surfaces [47]. These resources are frequently compiled in the annual Database Issue of Nucleic Acids Research.…”

Beyond Molecular Recognition: Using a Repulsive Field to Tune Interfacial Valency and Binding Specificity between Adhesive Surfaces

“…The majority of cellular adhesion molecules bind with energies near 10kT, making the individual bonds reversible. [65][66][67] Also worth mentioning is the importance of the binding kinetics. Binding and unbinding rate constants comprise a "state space" in which different families of adhesion molecules reside and accomplish their function.…”