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Related Experiment Videos

How well are protein structures annotated in secondary databases?

Kristian Rother1, Elke Michalsky, Ulf Leser

  • 1Berlin Center of Genome-Based Bioinformatics (BCB), Institute of Biochemistry at the Charité, Humboldt Universität Berlin, Berlin, Germany. kristian.rother@charite.de

Proteins
|July 16, 2005
PubMed
Summary
This summary is machine-generated.

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Protein Data Bank (PDB) entries show an annotation gap for recent structures in manually curated databases. While databases overlap well, a significant portion of PDB remains poorly annotated.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Database Annotation

Background:

  • The Protein Data Bank (PDB) is a crucial repository for structural biology data.
  • Annotation of PDB entries with external data enhances their utility for research.
  • Understanding the extent and patterns of PDB annotation is vital for data interpretation.

Purpose of the Study:

  • To quantify the level of second-party annotation in Protein Data Bank (PDB) entries.
  • To identify patterns in annotation based on structure age and database overlap.
  • To inform studies relying on PDB annotations by highlighting potential biases.

Main Methods:

  • Analysis of cross-references between PDB and 15 external databases.
  • Assessment of annotation status based on the age of PDB structures.

Related Experiment Videos

  • Evaluation of database overlap to determine coverage of PDB entries.

    • Main Results:

    • A significant 'annotation gap' exists for PDB structures less than 7 years old, particularly in manually curated secondary databases.
    • The 15 examined databases exhibit substantial overlap, effectively annotating approximately two-thirds of the PDB.
    • One-third of the PDB entries are identified as poorly annotated across the evaluated databases.

    Conclusions:

    • Recent PDB structures are less comprehensively annotated, posing challenges for studies dependent on up-to-date annotations.
    • The uneven annotation distribution across the PDB necessitates careful consideration during data selection for research.
    • Future efforts should aim to improve annotation of newer structures and address the poorly annotated segments of the PDB.