FireDB

FireDB catalogs catalytic and biologically relevant small ligand-binding residues derived from Protein Data Bank (PDB) structures to support functional analysis of proteins.

Key Features:

• Curated Ligand-Binding Residues: Manually curated biologically relevant small ligands extracted from PDB structures, representing a subset of contacting ligands.
• Cross-References and Annotations: Cross-references contacting small ligands to publicly available biological, chemical, and pharmacological databases, covering 95% of contacting small ligands.
• Biological Relevance Insights: Calculates biological relevance of individual binding sites using multiple sequence alignments generated from an all-against-all comparison of each FireDB binding site.
• Comprehensive Repository: Integrates ligand-binding residues filtered from atomic contacts in PDB crystal structures with reliably annotated catalytic residues from the Catalytic Site Atlas.

Scientific Applications:

• Protein Function Analysis: Enables identification and characterization of residues involved in ligand binding and catalysis to inform functional annotation of proteins with known structures.
• Drug Discovery and Pharmacology: Provides ligand-contact and pharmacological cross-reference information to support target assessment and ligand interaction studies.
• Comparative Protein Studies: Facilitates comparison of binding site similarity and residue variation across homologous proteins using binding-site alignments.

Methodology:

Filtering of atomic contacts from PDB crystal structures; incorporation of annotated catalytic residues from the Catalytic Site Atlas; all-against-all comparison of each FireDB binding site to generate multiple sequence alignments; cross-referencing contacting small ligands to external biological, chemical, and pharmacological databases.