Related Experiment Video
Updated: May 15, 2026
09:10
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
Trendspotting in the Protein Data Bank
Helen M Berman1, Buvaneswari Coimbatore Narayanan, Luigi Di Costanzo
1Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA. berman@rcsb.rutgers.edu
FEBS Letters
|January 23, 2013
Summary
The Protein Data Bank (PDB) archives over 85,000 macromolecule structures. Analyzing this data reveals trends to guide the future of structural biology and PDB data management.
Area of Science:
- Structural biology
- Biochemistry
- Bioinformatics
Background:
- The Protein Data Bank (PDB) was founded in 1971.
- It serves as a global archive for 3D structures of biological macromolecules.
- Over 85,000 structures are currently available.
Purpose of the Study:
- To analyze trends within the PDB archive.
- To inform the future direction of structural biology research.
- To optimize the management of the growing PDB dataset.
Main Methods:
- Data mining of the Protein Data Bank archive.
- Trend analysis of structural biology data.
- Bibliometric and structural data analysis.
Main Results:
- Identification of key trends in macromolecular structure determination.
- Insights into the evolution of structural biology.
- Assessment of current data management strategies.
Conclusions:
- Analysis of PDB data provides valuable insights for future research.
- Strategic planning is essential for managing large-scale biological data.
- Understanding historical trends aids in advancing structural biology.
Related Concept Videos
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...
02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...
01:24Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
01:13Protein Organization
Overview