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Related Concept Videos

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...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
Cofactors and Coenzymes01:24

Cofactors and Coenzymes

Enzymes are proteins made of amino acids. The functional group of each constituent amino acid catalyzes a wide variety of chemical reactions via ionic interactions or acid-base reactions. However, amino acids cannot catalyze oxidation-reduction and group transfer reactions and need to be aided by non-protein components called cofactors. Cofactors are also referred to as the chemical teeth of an enzyme.
Cofactors can be metallic ions or organic molecules called coenzymes. These types of helper...

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Related Experiment Video

Updated: Jun 23, 2026

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

COFECO: composite function annotation enriched by protein complex data.

Choong-Hyun Sun1, Min-Sung Kim, Youngwoong Han

  • 1Department of Bio and Brain Engineering, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, South Korea.

Nucleic Acids Research
|May 12, 2009
PubMed
Summary
This summary is machine-generated.

COFECO integrates protein complex, KEGG pathway, and Gene Ontology (GO) data for enhanced gene function annotation. This tool provides a consolidated view, improving the understanding of gene sets and their evolutionary conserved functions across species.

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Last Updated: Jun 23, 2026

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Functional enrichment tools often yield extensive, generalized annotations, hindering consolidated information retrieval.
  • Integrating protein-protein interaction data with pathways and Gene Ontology (GO) terms can clarify annotation interrelationships.

Purpose of the Study:

  • To develop COFECO, a web-based tool for composite annotation of protein complexes, KEGG pathways, and GO terms.
  • To improve the comprehensiveness and specificity of functional annotation for gene sets and their orthologs.

Main Methods:

  • Utilizes protein complex data, GO terms, and KEGG pathways as integrated annotation resources.
  • Employs orthology-based annotations across species to complement individual genome data.
  • Incorporates a term filtering feature for user-specified annotation retrieval.
  • Enables cross-comparison of annotation results between different datasets.

Main Results:

  • COFECO identifies composite annotation sets of correlated functions and cellular processes more comprehensively.
  • Orthology-based annotations reveal evolutionary conserved correlations and address data gaps.
  • The tool facilitates exploration through integrated GO hierarchical and KEGG pathway viewers.

Conclusions:

  • COFECO offers an advanced approach to functional annotation by integrating diverse biological data.
  • The tool enhances the specificity and interpretability of gene function analysis.
  • COFECO provides valuable insights into gene sets, their functions, and evolutionary conservation.