PDB-BRE

PDB-BRE extracts binding residues from 3D structures obtained from the RCSB Protein Data Bank (RCSB PDB) to analyze ligand–protein interactions.

Key Features:

• Comprehensive Ligand Support: Supports six ligand types: Proteins, Peptides, DNA, RNA, Mixed DNA/RNA entities, and Non-polymeric entities.
• Consideration of Inserted and Modified Residues: Accounts for inserted and modified residues within complexes when identifying interacting residues.
• Massively Parallel Batch Analysis: Optimized for high-throughput, massively parallel batch analysis of numerous ligand–protein complexes.
• Application to Novel Complexes: Can be applied to predict binding residues in novel or uncharacterized ligand–protein complexes.

Scientific Applications:

• Mechanistic Studies: Elucidating biological mechanisms of ligand–protein interactions by identifying binding residues.
• Drug Discovery: Identifying potential binding sites for therapeutic targeting and lead selection.
• Structural Bioinformatics and Molecular Biology: Supporting analyses of ligand specificity and protein function using structural data.

Methodology:

Automatically extracts interacting residues from 3D structures obtained from the RCSB PDB, handling multiple ligand types and inserted/modified residues and supporting massively parallel batch processing.