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oai:figshare.com:article/34028053 2026-09-29T22:04:37Z category_1 category_4 category_19 category_21 category_873 category_734 category_931 category_64 category_69 portal_63 item_type_3 month_year_09_2026

Evaluation of the Complementarity of Three Major Databases of Protein–Ligand Binding Affinity Data Haotian Gao (11051517) Fengfei Miao (19451491) Xinchong Chen (16379297) Jingyuan Li (53885) Kexin Wu (12111219) Yanbei Li (21425857) Yan Li (23143) Yifei Qi (551524) Zhen Duan (769189) Renxiao Wang (460970) Biophysics Biochemistry Pharmacology Biotechnology Chemical Sciences not elsewhere classified Biological Sciences not elsewhere classified Information Systems not elsewhere classified Cancer Inorganic Chemistry unique value makes two larger repositories three major databases selection strategies customized dimensional complex structures 40 %– 50 single resource achieves limited overlap arises drug discovery datasets data records sourced drug discovery data overlap adopt resource version 35 version 2025 version 2024 systematically cross merely 22 mandating researchers fundamental differences early stage distinct focuses data entries comprehensive coverage broader chemical biological landscape best suited based studies 08 ). Protein–ligand binding affinity data underpin a variety of tasks at the early stage of drug discovery. Public databases including ChEMBL, BindingDB, and PDBbind curate such data with distinct focuses, yet their data overlap and complementary attributes remain insufficiently quantified. In this work, we systematically cross-mapped protein–ligand binding data in PDBbind (version 2024) against data records sourced from ChEMBL (version 35) and BindingDB (version 2025.08). Our analysis revealed that merely 22.1% and 23.9% of PDBbind’s annotated protein–ligand complexes possess matching binding data records in ChEMBL and BindingDB, respectively, confirming that the PDBbind dataset is not a subset of the other two larger repositories. This limited overlap arises from fundamental differences in scope: ChEMBL and BindingDB center on drug discovery datasets, whereas the data entries in PDBbind encompass a broader chemical and biological landscape. Our analysis further uncovered substantial data redundancy in ChEMBL and BindingDB, where 40%–50% of protein–ligand interaction pairs are associated with multiple, discrepant binding affinity values. Currently, no single resource achieves a comprehensive coverage of available protein–ligand binding data, mandating researchers to adopt resource-selection strategies customized to their goals. While ChEMBL and BindingDB host extensive bioactivity archives, PDBbind directly links three-dimensional complex structures with carefully curated binding affinity data. This unique value makes it best suited for structure-based studies. 2026-09-29T00:00:00Z Dataset Dataset 10.1021/acs.jcim.6c02172.s001 https://figshare.com/articles/dataset/Evaluation_of_the_Complementarity_of_Three_Major_Databases_of_Protein_Ligand_Binding_Affinity_Data/34028053 CC BY-NC 4.0