eModel-BDB

eModel-BDB provides atomic-level comparative structure models of drug-protein interactions derived from Binding Database and Protein Data Bank (PDB) interaction data to support structure-based analyses and drug discovery.

Key Features:

• Dataset: The resource contains 200,005 comparative models derived from 1,391,403 interaction records from the Binding Database and the Protein Data Bank (PDB) as of January 31, 2017.
• Model types: Atomic-level models represent drug-bound proteins and drug-protein assemblies that lack experimentally determined structures.
• Modeling methods: Protein meta-threading and template-based structure modeling are used to generate comparative models.
• Refinement and binding-site analysis: Refinement processes and binding site detection are applied to improve structural detail and identify ligand interaction sites.
• Docking approach: Ligand similarity-based docking is employed to place drug-like molecules into modeled binding sites.
• Quality control and validation: Rigorous quality-control measures are implemented and weakly homologous models undergo retrospective validation against newly deposited experimental structural data in the PDB, assessing global protein structure and atomic details of bound ligands.

Scientific Applications:

• Structure-based drug discovery and repositioning: Provides modeled drug-bound protein structures to support identification of novel therapeutics and new uses for existing drugs.
• Drug target identification: Enables exploration of interactions between drug-like molecules and protein targets to prioritize candidate targets.
• Protein structure determination support: Supplies comparative models to aid prediction of protein structures that lack experimental resolution.

Methodology:

Comparative models were generated from Binding Database and PDB interaction data using protein meta-threading, template-based structure modeling, refinement processes, binding site detection, ligand similarity-based docking, and retrospective validation against newly deposited PDB structures.