Molecular_Interaction_Maps/ProteinDomains

TableOfContents([2])

Summary

A user wants to describe interactions of a protein, domain by domain.

Step-by-Step User Action

1. User specifies a protein to be described in more detail
2. User specifies the number of domains to be included
3. User specifies the name of each domain
4. User then uses each domain in subsequent reactions

Visual Aides

An example of the notation for specifying protein domains follows:

Requirements for Cytoscape

TBD

Importance

For some maps, the key proteins have several protein domains of interest, and modeling with that level of detail is important for the map.

Variations

The domain can interact as any other species. E.g. in this case, Dom3 of protein A binds to protein B.

The protein may be arranged vertically as well:

It is also possible to model a trans-membrane protein, in which some portions of the protein exist in one compartment, and some in another.

protein domains can interact with each other, for example, by binding:

Other Examples

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