PDBe

PDBe provides curated and remediated macromolecular structure data and derived annotations from the Protein Data Bank to support structural biology research and analysis.

Key Features:

• Archive curation and integration: Enhances quality and consistency of the Protein Data Bank archive in collaboration with Worldwide PDB partners and the European Bioinformatics Institute.
• Remediated and derived data: Leverages remediated PDB archive data and curates actively maintained derived data.
• Advanced database infrastructure: Implements a database infrastructure to store and index structural and derived data.
• Specialized interaction database: Stores detailed information about interactions between proteins and bound molecules.
• Query capabilities: Supports simple textual queries and complex 3D structure-based inquiries.
• PDBeView Atlas pages: Provides PDBeView Atlas pages that summarize individual PDB entries and aggregate associated data.
• Deposition and analysis tools: Develops tools for structure deposition and analysis informed by X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and cryo-Electron Microscopy (cryo-EM) communities.

Scientific Applications:

• Structural data dissemination: Provision of curated macromolecular structures and annotations from the Protein Data Bank for research and analysis.
• Protein–ligand interaction analysis: Analysis and retrieval of detailed interactions between proteins and bound molecules.
• Deposition and validation workflows: Support for structure deposition and analysis workflows arising from X-ray crystallography, NMR spectroscopy, and cryo-EM communities.
• 3D structure-based research: Enabling complex 3D structure-based inquiries for structural comparison and analysis.
• Archive quality assurance: Activities to improve the quality and consistency of the PDB archive.

Methodology:

Uses an advanced database infrastructure that leverages remediated PDB archive data alongside a specialized interaction database to support textual and 3D structure-based queries, and exposes PDBeView Atlas pages summarizing individual PDB entries.