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Structural database resources for biological macromolecules.

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    |June 9, 2016
    PubMed
    Summary
    This summary is machine-generated.

    This review highlights curated Protein Data Bank (PDB) databases, offering enhanced tools for exploring protein structures and interactions. These specialized resources provide superior data quality for biological macromolecule research compared to raw PDB entries.

    Keywords:
    PDB miningdynamicsinteractionsligand bindingnucleic acidsprotein

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    Area of Science:

    • Structural Biology
    • Bioinformatics
    • Computational Biology

    Background:

    • The worldwide Protein Data Bank (PDB) is a primary resource for protein structure data.
    • Raw PDB entries can be overwhelming and contain redundancies or errors, hindering efficient analysis.
    • Specialized databases derived from PDB offer curated and enhanced data for specific research needs.

    Purpose of the Study:

    • To review and categorize currently active, up-to-date databases derived from the PDB.
    • To facilitate the discovery and utilization of these specialized databases for researchers.
    • To highlight the advantages of using curated databases over raw PDB entries for structural studies.

    Main Methods:

    • Systematic review of PDB-derived databases.
    • Categorization of databases based on their functionalities (e.g., browsing, analysis, specific molecule types).
    • Inclusion of web servers and discussion of valuable discontinued databases.

    Main Results:

    • Identification of diverse PDB-derived databases with tailored visualization and analysis tools.
    • Databases offer curated data, error checking, and removal of sequence redundancy for improved mining.
    • Examples demonstrate enhanced utility for structural studies and advancing knowledge of biological macromolecules.

    Conclusions:

    • Curated PDB-derived databases significantly improve the efficiency and accuracy of structural biology research.
    • These specialized resources provide valuable insights and are often more informative than raw PDB data.
    • Researchers are encouraged to leverage these databases for advanced structural and functional studies.