firedb WS

firedb WS curates catalytic and biologically relevant small ligand-binding residues from Protein Data Bank (PDB) structures and integrates chemical and pharmacological annotations for those ligands.

Key Features:

• Curated binding residues: Manually curated catalytic and biologically relevant small ligand-binding residues extracted from PDB structures.
• Ligand cross-referencing: Provides external references for 95% of small ligands that contact proteins, integrating annotations from publicly available biological, chemical, and pharmacological compound databases.
• Binding-site relevance scoring: Assesses the biological relevance of individual binding sites using multiple sequence alignments derived from all-against-all comparisons within the database.
• Pharmacological annotations: Aggregates pharmacological and chemical information linked to PDB ligands from external compound databases.
• Data export format: Supports data export in MySQL format.

Scientific Applications:

• Protein–ligand interaction analysis: Annotation and analysis of catalytic and small ligand-binding residues in structural data from the PDB.
• Functional site interpretation: Interpreting functional implications of binding sites based on conservation and relevance metrics from multiple sequence alignments.
• Pharmacology and drug discovery: Mapping PDB ligands to pharmacological and chemical databases to support drug-discovery and pharmacological research.
• Structural biology and biochemistry: Providing curated ligand-binding residue information for structural and biochemical studies.

Methodology:

The database computes binding-site biological relevance via multiple sequence alignments produced from all-against-all comparisons of each binding site and integrates external compound annotations by cross-referencing public biological, chemical, and pharmacological databases.