Diff for "Molecular_Interaction_Maps/ProteinDomains"

Differences between revisions 1 and 4 (spanning 3 versions)

Use Case Name : ../ProteinDomains

For Feature : MIMEditor

Editors: DavidKane

TableOfContents([2])

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

PageComment2

Molecular_Interaction_Maps/ProteinDomains (last edited 2009-02-12 01:03:02 by localhost)

-  ← Revision 1 as of 2006-11-15 20:42:27 →
  Size: 2879
  Editor: lfrq80
  Comment:
+  ← Revision 4 as of 2006-11-17 20:29:26 →
  Size: 3521
  Editor: lfrq80
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+## page was renamed from ProteinDomains
-Line 7:
+Line 8:
-|| '''Use Case Name''' : ProteinDomains ||
+|| '''Use Case Name''' : ../ProteinDomains ||
-Line 34:
+Line 35:
+attachment:proteindomains1_061117_dwk.PNG
-Line 46:
+Line 49:
+attachment:proteindomains2_061117_dwk.PNG
-Line 49:
+Line 54:
-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:proteindomains3_061117_dwk.PNG



It is also possible to model a trans-membrane protein, in which some portions of the protein exist in one Self:Compartment, and some in another.
-Line 51:
+Line 58:
+attachment:proteindomains4_061117_dwk.PNG
-Line 52:
+Line 60:
+Earlier maps have the same concept with a slightly different graphical style, as in this example:
-Line 53:
+Line 62:
-protein domains can interact with each other, for example, by binding:
+attachment:proteindomains7_061117_dwk.PNG
-Line 55:
+Line 64:
+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
-Line 61:
+Line 77:
-Shared MimEditorUseCaseComments
+Shared ../MimEditorUseCaseComments