title: Cross-Mapping of Protein - Ligand Binding Data Between ChEMBL and PDBbind.
abstract: The ChEMBL database is a valuable open data source, which provides a comprehensive collection of binding data, functional and ADMET properties of bioactive compounds. The PDBbind database has a more focused scope, i.e. collecting binding data for the protein-ligand complexes in the Protein Data Bank. Currently, the PDBbind collection of binding data is rather modest as compared to the ChEMBL collection (∼13 000 versus ∼1.3 million). One may suspect if the former is actually a subset of the latter. In this study, we mapped the molecular information and protein-ligand binding data in PDBbind to the records in ChEMBL, and then analyzed the overlap between the binding data recorded in these two databases. Our results indicate that only ∼20 % of the binding data in PDBbind can find their counterparts in ChEMBL. Thus, the PDBbind collection of binding data is largely complementary to the ChEMBL collection. We also reveal two reasons accounting for the low overlap between two databases: First, only a minor fraction of the protein-ligand complexes in PDBbind is covered by ChEMBL; Second, the literature spaces screened by these two databases do not have a substantial overlap either. The value of focused databases versus more comprehensive ones is demonstrated by our study.
authors.affiliation: State Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China phone:+86-21-54925128.
authors.forename: Zhihai
authors.initials: Z
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China phone:+86-21-54925128.
authors.forename: Jie
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China phone:+86-21-54925128.
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China phone:+86-21-54925128.
authors.forename: Yuchen
authors.initials: Y
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China phone:+86-21-54925128.
authors.forename: Wei
authors.initials: W
authors.lastname: Nie
authors.affiliation: State Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China phone:+86-21-54925128.
authors.forename: Li
authors.initials: L
authors.lastname: Han
authors.affiliation: State Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China phone:+86-21-54925128.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, P. R. China phone:+86-21-54925128. wangrx@mail.sioc.ac.cn.|State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, P.R. China. wangrx@mail.sioc.ac.cn.
authors.forename: Renxiao
authors.initials: R
authors.lastname: Wang
mesh_terms: D030562:Databases, Protein; D008024:Ligands
chemical_list: D008024:Ligands
keywords: Binding data; Drug discovery; Proteinligand complex; Public database