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Related Concept Videos

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 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
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...
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
09:51

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

Published on: July 16, 2017

PDBpaint, a visualization webservice to tag protein structures with sequence annotations.

David Fournier1, Miguel A Andrade-Navarro

  • 1Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany. david.fournier@mdc-berlin.de

Bioinformatics (Oxford, England)
|July 16, 2011
PubMed
Summary
This summary is machine-generated.

PDBpaint visualizes protein sequence features on 3D structures, aiding function and prediction analysis. This tool integrates bioinformatics data for enhanced protein structure interpretation.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Protein features are typically shown on linear amino acid sequences.
  • These features exist in three-dimensional (3D) space within folded proteins.

Purpose of the Study:

  • To develop a tool for mapping protein sequence features onto their 3D structures.
  • To aid in understanding feature function and evaluating sequence/structural predictions.

Main Methods:

  • Developed PDBpaint, a tool utilizing the Jmol Java viewer for interactive 3D protein structure visualization.
  • Integrated annotations from bioinformatics resources like Pfam, UniProt, TMHMM2.0, and SignalP.
  • Enabled manual addition of custom annotations.

Main Results:

  • PDBpaint successfully displays sequence-based annotations on 3D protein structures.
  • The tool supports both existing and user-provided protein structures.
  • Facilitates visualization of various protein feature types.

Conclusions:

  • PDBpaint simplifies the interpretation of protein structure-function relationships.
  • It serves as a valuable resource for researchers analyzing protein sequences and structures.
  • The tool enhances the utility of bioinformatics data by contextualizing it within 3D protein models.