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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...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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 to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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 to...

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Related Experiment Video

Updated: Jun 20, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells

Published on: March 3, 2015

NASCENT: an automatic protein interaction network generation tool for non-model organisms.

Daniel Banky1, Rafael Ordog, Vince Grolmusz

  • 1Protein Information Technology Group, Eotvos University, H-1117 Budapest, Hungary.

Bioinformation
|August 27, 2009
PubMed
Summary

This study introduces NASCENT, an automated tool for generating protein interaction networks for non-model organisms. It overcomes data limitations, enabling broader systems biology research.

Keywords:
interactionmodelnetworkproteintool

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Public protein interaction databases primarily cover model organisms.
  • Limited data exists for protein interactions in non-model organisms.
  • This gap hinders comprehensive systems biology studies.

Purpose of the Study:

  • To present NASCENT, an automated tool for modeling protein interaction networks.
  • To enable network generation for organisms with sparse interaction data.
  • To facilitate broader applications of systems biology approaches.

Main Methods:

  • NASCENT utilizes gene-name mapping for network modeling.
  • It is available as a web-based tool and a downloadable Java program.
  • Outputs include graphical and computer-readable network formats.

Main Results:

  • NASCENT successfully models protein interaction networks for non-model organisms.
  • The tool generates networks applicable to existing network modeling software.
  • It provides a solution for the scarcity of protein interaction data.

Conclusions:

  • NASCENT significantly advances the study of protein interactions in underrepresented organisms.
  • The tool democratizes network modeling for a wider range of species.
  • It supports comparative and functional genomics research.