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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...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Proteomics01:33

Proteomics

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.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Related Experiment Video

Updated: Jun 8, 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

Protein-protein interaction and pathway databases, a graphical review.

Tomas Klingström1, Dariusz Plewczynski

  • 1Uppsala University.

Briefings in Bioinformatics
|September 21, 2010
PubMed
Summary
This summary is machine-generated.

Researchers can now easily survey protein-protein interaction (PPI) databases. A new graphical tool simplifies accessing and understanding PPI data, saving valuable research time.

More Related Videos

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Related Experiment Videos

Last Updated: Jun 8, 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

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • The volume of protein-protein interaction (PPI) data at the proteomic scale is rapidly expanding.
  • Numerous databases now provide access to this information, leading to diverse data delivery methods.
  • This proliferation creates a significant time barrier for researchers needing an overview of available PPI resources.

Purpose of the Study:

  • To provide researchers with a valuable tool for surveying protein-protein interaction databases.
  • To reduce the time required to gain a broad understanding of available PPI resources.
  • To offer a graphical representation of data exchange between PPI databases.

Main Methods:

  • A comprehensive survey of protein-protein interaction databases was conducted.
  • Data exchange formats and accessibility were analyzed.
  • A graphical representation of data exchange was developed in collaboration with www.pathguide.org.
  • A Cytoscape web implementation was utilized for visualization.
  • Downloadable Cytoscape cys files were made available.

Main Results:

  • A consolidated overview of protein-protein interaction databases is now available.
  • A graphical tool aids in understanding data exchange across PPI databases.
  • The resource is accessible via a Cytoscape web implementation at http://www.pathguide.org/interactions.php.
  • Local Cytoscape files can be downloaded from http://bio.icm.edu.pl/~darman/ppi.

Conclusions:

  • This survey and accompanying graphical tool significantly streamline the process of exploring protein-protein interaction databases.
  • Researchers can more efficiently access and interpret proteomic interaction data.
  • The developed resource facilitates a better understanding of the PPI database landscape.