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Related Concept Videos

Protein and Protein Structures02:15

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Protein Organization01:24

Protein 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.
Protein Organization01:13

Protein Organization

Overview
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Protein Families02:47

Protein 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...
Protein Families02:47

Protein 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...

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.

Akira R Kinjo1, Hirofumi Suzuki, Reiko Yamashita

  • 1Institute for Protein Research and Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

Nucleic Acids Research
|October 7, 2011
PubMed
Summary

Protein Data Bank Japan (PDBj) manages macromolecular structure data and offers analysis tools. They developed PDB/RDF, integrating PDB data with other biological resources using Semantic Web standards.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Data Archiving

Background:

  • Protein Data Bank Japan (PDBj) is a key member of the worldwide Protein Data Bank (wwPDB).
  • PDBj archives experimentally determined macromolecular structures and provides analytical tools.
  • Interoperability of biological data is crucial for advancing research.

Purpose of the Study:

  • To summarize the services and tools offered by PDBj for protein structure and function analysis.
  • To introduce PDB/RDF, a new data format for enhanced data integration.
  • To facilitate the integration of PDB data with other biological information resources.

Main Methods:

  • Development of PDB/RDF using Resource Description Framework (RDF) format.
  • Creation of an ontology in Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary.
  • Utilizing Semantic Web standards for data representation.

Main Results:

  • PDBj offers a comprehensive suite of tools for analyzing protein structures and functions.
  • PDB/RDF and its associated ontology are now available.
  • The new format enhances data interoperability and integration capabilities.

Conclusions:

  • PDB/RDF provides a standardized format for Semantic Web integration of PDB data.
  • This development significantly improves the ability to connect PDB information with other biological databases.
  • PDBj continues to enhance access to and utility of structural biology data.