PDB-2-PB

PDB-2-PB provides curated Protein Block (PB) sequences and associated backbone dihedral angles for protein structures from the Protein Data Bank (PDB) to support analysis of protein conformations and protein–nucleic acid interactions.

Key Features:

• Database content (PDB-2-PBv3.0): PB sequences for 147,602 PDB structures encompassing 400,355 protein chains (October 2019).
• Protein Block sequences and dihedral angles: PB sequences and associated backbone dihedral angles linked to PDB structure records.
• Coverage of incomplete chains: PB information is provided for protein chains that have missing atom records within PDB entries.
• Integration of nucleic acid interactions and functional classification: Protein interaction data involving DNA and RNA and corresponding functional classifications from the Nucleic Acid Database (NDB) and PDB are integrated.
• Curated expansion: The v3.0 release represents a two-fold increase in protein structures and a four-fold increase in protein chains relative to the previous version.

Scientific Applications:

• Protein conformation analysis: Use of PB sequences and dihedral angles to analyze local structural motifs and backbone conformations.
• Protein–nucleic acid interaction studies: Characterization of protein interactions with DNA and RNA using integrated interaction annotations and functional classifications.
• Large-scale comparative studies: Comparative and statistical analyses across 147,602 PDB structures and 400,355 chains to assess conformational variability.
• Computational structural biology: Support for computational analyses and modeling workflows that require PB-based representation or dihedral-angle annotations.

Methodology:

Curation associates PB sequences and backbone dihedral angles with PDB coordinates, integrates interaction and functional annotations from NDB and PDB, and retains PB records for chains with missing atom records.