HProteome-BSite

HProteome-BSite predicts ligand binding sites across the human proteome using model structures from the AlphaFold Protein Structure Database to characterize protein–ligand interactions for functional annotation and drug discovery.

Key Features:

• AlphaFold model structures: Uses model structures from the AlphaFold Protein Structure Database as the structural basis for binding-site prediction.
• Refined GalaxySite (template-based): Employs a refined version of the template-based GalaxySite method to predict ligand binding sites.
• High-confidence structural domains: Processes model structures into high-confidence structural domains to improve coverage and precision of predictions.
• Predicted ligands and binding poses: Provides predicted ligands and their binding poses for identified binding sites.
• Proteome coverage: Includes predictions for 80.74% of UniProt entries within the AlphaFold human 3D proteome.
• Atomic-level interaction detail: Characterizes protein–ligand interactions at atomic resolution.

Scientific Applications:

• Protein functional annotation: Supports annotation of protein function through identification of ligand-binding sites.
• Identification of regulatory molecules: Aids identification of potential regulatory small molecules and ligands interacting with human proteins.
• Drug discovery and target identification: Facilitates identification and prioritization of therapeutic targets and assessment of ligand binding poses for lead discovery.
• Structural analysis of interfaces: Informs structural studies of protein–ligand interfaces at atomic detail.

Methodology:

Uses model structures from the AlphaFold Protein Structure Database, processes structures into high-confidence structural domains, and applies a refined, template-based GalaxySite method to predict ligand binding sites and binding poses.