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Related Concept Videos

Protein Networks02:26

Protein Networks

4.6K
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,...
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Protein Networks02:26

Protein Networks

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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

3.0K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
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Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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ANAT 2.0: reconstructing functional protein subnetworks.

Yomtov Almozlino1, Nir Atias1, Dana Silverbush1

  • 1School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.

BMC Bioinformatics
|November 18, 2017
PubMed
Summary
This summary is machine-generated.

ANAT 2.0 is an updated tool for reconstructing protein networks. This enhanced version offers new algorithms and database updates, improving its applicability to diverse biological datasets and addressing reconstruction challenges across species.

Keywords:
Cytoscape pluginNetwork inferenceProtein-protein interaction networkSubnetwork reconstruction

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • ANAT is a Cytoscape-based tool for inferring protein-protein interaction networks.
  • It supports network reconstruction across various biological scenarios and organisms like yeast and human.

Purpose of the Study:

  • To introduce ANAT 2.0, a significantly updated version of the protein network inference tool.
  • To enhance the tool's capabilities and applicability to a broader range of biological data.

Main Methods:

  • Development of ANAT 2.0 with substantial code and database updates.
  • Integration of several new network reconstruction algorithms.

Main Results:

  • ANAT 2.0 offers extended applicability to diverse biological datasets.
  • The updated tool addresses multiple challenges in network reconstruction.

Conclusions:

  • ANAT 2.0 is a current and improved network reconstruction tool.
  • It effectively tackles reconstruction challenges across multiple species, enhancing biological data analysis.