ccPDB

ccPDB compiles and provides curated datasets from the Protein Data Bank (PDB) and published literature to support development and application of computational methods for protein structure and function annotation.

Key Features:

• Data Compilation: Aggregates curated datasets derived from published research and directly extracted from PDB releases using standardized protocols.
• Custom Dataset Creation: Provides a module to create customized datasets from the current PDB release via a defined six-step procedure.
• Integrated Web Services: Includes computational job submission on PDB-based servers, protein structure annotation tools, and pattern generation for recurring structural motifs and functional sites.
• Diverse Dataset Types: Maintains over 30 dataset types including secondary structure elements, tight-turns, nucleotide- and metal-interacting residues, and DNA/RNA binding residues.

Scientific Applications:

• Method development: Supports training and benchmarking of computational methods for protein structure and function annotation.
• Comparative structural analysis: Enables comparative studies of structural motifs across different proteins.
• Functional interaction analysis: Facilitates analysis of interaction sites with nucleotides, metals, and nucleic acids.

Methodology:

Datasets are compiled from literature and extracted from PDB releases using standardized protocols; custom datasets are produced via a six-step procedure; integrated services perform computational job submission, structure annotation, and pattern generation.