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The protein protein interactions are displayed in a signed network that describes what type of interactions that are taking place [74] Protein–protein interactions often result in one of the interacting proteins either being 'activated' or 'repressed'. Such effects can be indicated in a PPI network by "signs" (e.g. "activation" or "inhibition").
In molecular biology, an interactome is the whole set of molecular interactions in a particular cell.The term specifically refers to physical interactions among molecules (such as those among proteins, also known as protein–protein interactions, PPIs; or between small molecules and proteins [1]) but can also describe sets of indirect interactions among genes (genetic interactions).
This method can be used to investigate protein-protein interactions, as well as to investigate modulators of protein-protein interactions by assessing ternary complex formation. An example for such modulators are PROTACs, which are investigated for their therapeutic potential in cancer therapy.
The WW domain [2] (also known as the rsp5-domain [3] or WWP repeating motif [4]) is a modular protein domain that mediates specific interactions with protein ligands. This domain is found in a number of unrelated signaling and structural proteins and may be repeated up to four times in some proteins.
Glycan-protein interactions may be detected by testing proteins of interest (or libraries of those) that bear fluorescent tags. The structure of the glycan-binding protein may be deciphered by several analytical methods based on mass-spectrometry , including MALDI-MS , LC-MS , tandem MS-MS , and/or 2D NMR .
The Database of Interacting Proteins (DIP) is a biological database which catalogs experimentally determined interactions between proteins. [ 2 ] [ 3 ] It combines information from a variety of sources to create a single, consistent set of protein–protein interactions.
Protein–protein interaction prediction is a field combining bioinformatics and structural biology in an attempt to identify and catalog physical interactions between pairs or groups of proteins. Understanding protein–protein interactions is important for the investigation of intracellular signaling pathways, modelling of protein complex ...
Since its inception, the MWC framework has been extended and generalized. Variations have been proposed, for example to cater for proteins with more than two states, [17] proteins that bind to several types of ligands [18] [19] or several types of allosteric modulators [19] and proteins with non-identical subunits or ligand-binding sites. [20]