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Related Concept Videos

Protein Networks02:26

Protein Networks

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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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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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Proteomics01:33

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying

P Zhang1, L Tao2, X Zeng1

  • 1Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore.

Journal of Molecular Biology
|October 16, 2016
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Summary

Researchers enhanced the PROFEAT web server to compute 329 network descriptors for biological networks. This tool aids systems-level investigations of protein, gene, and disease interactions.

Keywords:
Web serverbiological networkbiological pathwaynetwork descriptorprotein descriptor

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Network science

Background:

  • Systems-level investigations using computational tools are crucial for studying biological, disease, and pharmacological networks.
  • Network descriptors from other disciplines are increasingly applied to biological networks like protein-protein interaction, gene regulatory, metabolic, and disease networks.
  • Existing public web servers for computing network descriptors often lack coverage for those relevant to biological studies.

Purpose of the Study:

  • To upgrade the PROFEAT web server for comprehensive computation of network descriptors.
  • To expand the repertoire of network descriptors available for biological network analysis.
  • To facilitate systems-level investigations of complex biological networks.

Main Methods:

  • The PROFEAT web server was upgraded to compute up to 329 network descriptors and protein-protein interaction descriptors.
  • The server computes descriptors for various network types: unweighted, edge-weighted, node-weighted, edge-node-weighted, and directed networks.
  • Network descriptors capture topological and connectivity characteristics.

Main Results:

  • The upgraded PROFEAT web server now offers computation of 329 network descriptors.
  • The server provides comprehensive characterization of network topological and connectivity properties.
  • The tool supports analysis of diverse biological network types.

Conclusions:

  • The enhanced PROFEAT web server provides a valuable resource for systems-level analysis of biological networks.
  • The expanded set of network descriptors facilitates deeper understanding of complex biological systems.
  • This tool aids researchers in studying genome, interactome, transcriptome, metabolome, and diseasome profiles.