Supporting data for "eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database"

Dataset type: Software
Data released on July 16, 2018

Naderi M; Govindaraj RG; Brylinski M (2018): Supporting data for "eModel-BDB: A database of comparative structure models of drug-target interactions from the Binding Database" GigaScience Database.


The structural information on proteins in their ligand-bound conformational state is invaluable for protein function studies and rational drug design. Compared to the number of available sequences, the repertoire of the experimentally determined structures of holo-proteins is not only limited, but also these structures do not always include pharmacologically relevant compounds at their binding sites. In addition, binding affinity databases provide vast quantities of information on interactions between drug-like molecules and their targets, however, often lacking structural data. On that account, there is a need for computational methods to complement existing repositories by constructing the atomic-level models of drug-protein assemblies that will not be determined experimentally in the near future. We created eModel-BDB, a database of 200,005 comparative models of drug-bound proteins based on 1,391,403 interaction data obtained from the Binding Database and the PDB library of January 31, 2017. Complex models in eModel-BDB were generated with a collection of the state-of-the-art techniques, including protein meta-threading, template-based structure modeling, refinement and binding site detection, and ligand similarity-based docking. In addition to a rigorous quality control maintained during dataset generation, a subset of weakly homologous models were selected for the retrospective validation against experimental structural data recently deposited to the Protein Data Bank. Validation results indicate that eModel-BDB contains models that are accurate not only at the global protein structure level, but also with respect to the atomic details of bound ligands. Freely available eModel-BDB can be used to support structure-based drug discovery and repositioning, drug target identification, and protein structure determination.

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Funding body Awardee Award ID Comments
National Institute of Health M Brylinski R35GM119524 National Institute of General Medical Sciences
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