PDBSiteScan

PDBSiteScan identifies three-dimensional protein fragments by comparing them to curated functional sites in the PDBSite database to enable structural annotation of protein function.

Key Features:

• PDBSite database: Contains over 8,100 curated functional sites derived from automated processing of the Protein Data Bank (PDB).
• Site types: Includes active sites, binding sites, posttranslational modification sites, and protein-protein interaction sites identified through analysis of atom coordinates in heterocomplexes.
• Functional categorization: Categorizes functional sites into more than 80 distinct groups for targeted structural comparisons.
• Automated 3D fragment search: Performs automated searches for three-dimensional protein fragments that align with reference sites.
• Maximum distance mismatch (MDM) criterion: Uses the MDM criterion to define acceptable structural deviation between query fragments and reference sites.
• Atomic-level comparison: Measures structural deviation specifically between the N, Cα, and C atoms of fragments and reference sites.
• Amino acid matching requirement: Requires perfect amino acid identity between the query fragment and the reference site for a match.

Scientific Applications:

• Structural biology: Annotates tertiary-structure-derived functional sites in protein structures.
• Bioinformatics: Integrates curated 3D site comparisons into structural analysis workflows.
• Molecular biology: Supports interpretation of structure-function relationships at the residue level.
• Drug discovery: Identifies structural motifs corresponding to ligand-binding or active sites relevant to drug design.
• Enzyme engineering: Detects conserved catalytic or binding site fragments for enzyme modification efforts.
• Protein-protein interaction studies: Reveals structural fragments associated with interaction interfaces.

Methodology:

Automated processing of PDB entries yields >8,100 functional sites; atom-coordinate analysis of heterocomplexes identifies site residues; automated searches compare 3D protein fragments to reference sites using the maximum distance mismatch (MDM) criterion with deviations measured for N, Cα, and C atoms and require perfect amino acid matching.