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Related Concept Videos

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 Networks02:26

Protein 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,...
Protein Networks02:26

Protein 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,...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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.

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

PDBe: Protein Data Bank in Europe.

S Velankar1, Y Alhroub, C Best

  • 1Protein Data Bank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Nucleic Acids Research
|November 24, 2011
PubMed
Summary
This summary is machine-generated.

The Protein Data Bank in Europe (PDBe) enhances access to biomacromolecular structure data. New tools like PDBportfolio and UniPDB improve visualization and data exploration for researchers.

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09:37

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Biotechnology

Background:

  • The Protein Data Bank in Europe (PDBe) is a key partner in the Worldwide Protein Data Bank (wwPDB) organization.
  • PDBe manages the global archive of biomacromolecular structure data.
  • There is a continuous need to improve accessibility of structural data for the biomedical community.

Purpose of the Study:

  • To describe recently developed, extended, or improved services by PDBe.
  • To enhance the accessibility and utility of biomacromolecular structure data.
  • To support researchers in the biomedical community through advanced data visualization and exploration tools.

Main Methods:

  • Development of an animated structure-presentation widget (PDBportfolio).
  • Creation of a widget to display UniProt sequence coverage in the Protein Data Bank (PDB) (UniPDB).
  • Implementation of chemistry- and taxonomy-based PDB archive browsers (PDBeXplore).
  • Development of an interactive visualization tool for NMR structures and associated data (Vivaldi).

Main Results:

  • PDBe has successfully developed and deployed new tools to aid in the exploration of structural data.
  • PDBportfolio offers animated presentations of molecular structures.
  • UniPDB provides graphical visualization of sequence coverage.
  • PDBeXplore enables browsing the PDB archive by chemical and taxonomic classifications.
  • Vivaldi facilitates interactive visualization of NMR data and analysis results.

Conclusions:

  • The newly developed and improved services by PDBe significantly enhance the accessibility of biomacromolecular structure data.
  • These tools empower the biomedical community with advanced capabilities for data analysis, visualization, and exploration.
  • PDBe continues to play a vital role in advancing structural biology research through innovative resource development.