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| || '''Use Case Name''' : ProteinDomains || | || '''Use Case Name''' : ../ProteinDomains || |
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attachment:proteindomains4_061117_dwk.PNG Earlier maps have the same concept with a slightly different graphical style, as in this example: attachment:proteindomains7_061117_dwk.PNG |
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attachment:proteindomains5_061117_dwk.PNG If a protein is described with domain detail, but it is unknown which domain an interaction is involved with, then the interaction is linked to the name of the protein instead: attachment:proteindomains6_061117_dwk.PNG |
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| Shared MimEditorUseCaseComments | Shared ../MimEditorUseCaseComments |
Summary
A user wants to describe interactions of a protein, domain by domain.
Step-by-Step User Action
- User specifies a protein to be described in more detail
- User specifies the number of domains to be included
- User specifies the name of each domain
- User then uses each domain in subsequent reactions
Visual Aides
An example of the notation for specifying protein domains follows:
attachment:proteindomains1_061117_dwk.PNG
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.
attachment:proteindomains2_061117_dwk.PNG
The protein may be arranged vertically as well:
attachment:proteindomains3_061117_dwk.PNG
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.
attachment:proteindomains4_061117_dwk.PNG
Earlier maps have the same concept with a slightly different graphical style, as in this example:
attachment:proteindomains7_061117_dwk.PNG
Protein domains can interact with each other, for example, by binding:
attachment:proteindomains5_061117_dwk.PNG
If a protein is described with domain detail, but it is unknown which domain an interaction is involved with, then the interaction is linked to the name of the protein instead:
attachment:proteindomains6_061117_dwk.PNG
Other Examples
Comments
Shared ../MimEditorUseCaseComments