Related Experiment Video
Updated: Jun 6, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
A series of PDB related databases for everyday needs
Robbie P Joosten1, Tim A H te Beek, Elmar Krieger
1Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
Nucleic Acids Research
|November 13, 2010
Summary
New databases complement the Protein Data Bank (PDB), offering enhanced protein structure analysis. These resources provide secondary structure, quality reports, sequence alignments, and re-refined structures for diverse biological research.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- The Protein Data Bank (PDB) is a primary global repository for macromolecular structure data.
- Analyzing protein structures requires access to diverse, well-curated information beyond raw atomic coordinates.
Purpose of the Study:
- To introduce a suite of parallel databases that augment the PDB.
- To provide enriched data for comprehensive protein structure analysis.
Main Methods:
- Development of parallel databases including DSSP (secondary structure), PDBREPORT (quality assessment), HSSP (sequence alignment), PDBFINDER (summaries), PDB_REDO (re-refined structures), and WHY_NOT (exclusion reasons).
- Weekly updates ensure data freshness and relevance.
Main Results:
- Each parallel database offers specialized information linked to PDB entries.
- These systems provide readily accessible, parsed, and enhanced structural data.
Conclusions:
- The presented databases offer valuable, integrated resources for researchers.
- These tools facilitate advanced analysis in structural genomics, cancer biology, and protein design.
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01:57Gene Families
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Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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