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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 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-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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

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Related Experiment Video

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

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RING: networking interacting residues, evolutionary information and energetics in protein structures.

Alberto J M Martin1, Michele Vidotto, Filippo Boscariol

  • 1Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.

Bioinformatics (Oxford, England)
|April 16, 2011
PubMed
Summary

We introduce RING, a web server for building protein residue interaction networks (RINs) from PDB files. RING integrates structural and conservation data for enhanced protein analysis and visualization.

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Published on: July 16, 2017

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Area of Science:

  • Structural bioinformatics
  • Network science in biology
  • Protein structure-function relationships

Background:

  • Residue Interaction Networks (RINs) model protein 3D structures as graphs.
  • Topological network parameters in RINs correlate with protein structure and function.
  • Existing methods lack interactive construction and integration of diverse data types.

Purpose of the Study:

  • To present RING, a novel web server for constructing and visualizing protein RINs.
  • To enable interactive generation of physico-chemically valid RINs from PDB files.
  • To facilitate the integration of structural, conservation, and energy-based data.

Main Methods:

  • Development of a web server (RING) for RIN construction.
  • Interactive generation of RINs from Protein Data Bank (PDB) files.
  • Integration of secondary structure, solvent accessibility, residue conservation, and energy scores.

Main Results:

  • RING enables interactive construction of RINs with integrated data.
  • RINs can be visualized in the Cytoscape platform.
  • The server facilitates analysis of protein active sites, demonstrated with glutathione peroxidase.

Conclusions:

  • RING provides a user-friendly platform for generating and analyzing protein RINs.
  • Integration of multiple data types enhances the biological insights derived from RINs.
  • The server supports advanced network analysis through Cytoscape plugins.