## page was renamed from CovalentBinding
## These are wiki comments - leave them in so that people can see them when editing the page

## This template may be useful for documenting use cases 
## Developed in response to a hackathon request for formalized, detailed use cases 
##  to help direct implementation proposals

|| '''Use Case Name''' : ../CovalentBinding ||
|| '''For Feature''' : [[MIMEditor]]||
|| '''Editors''': DavidKane ||

## EXAMPLE: 
## Use Case Name: Representation of Protein Complex
## For Feature: Grouping Function
## Editors: Mr. Knowitall

<<TableOfContents([2])>>

== Summary ==
## Provide a one paragraph description of the use case
A user wants to describe the possibility that a small molecule is covalently bound to large molecule or another small molecule.

== Step-by-Step User Action ==
## Provide a step-by-step account of how the user would execute the use case.  For example: (1) right click on node, (2) choose "expand" from context menu, (3) new view is created, etc...

 1. User specifies a protein to be involved in the interaction
 1. User specifies the molecule to be bound
 1. User specifies that protein to be covalently bound to the protein
 1. User optionally specifies the evidence for this reaction

== Visual Aides ==
## Provide attachments to images to illustrate the use case (screenshots, mock-ups, storyboards, etc)
The Kohn notation for this reaction is the following:  

{{attachment:covalentbinding1_061115_dwk.png}}

An example showing the binding of a phosphate to a protein follows:

{{attachment:covalentbinding2_061115_dwk.png}}

The color in this example is convention, and is not an essential element in the notation.

== Requirements for Cytoscape ==
## List the components/functions already in Cytoscape that are relevant to the use case and possible implementations (e.g., "current context menus can be used accomplish step 2 above")
## Also list components/functions that are needed in Cytoscape to execute the use case (e.g., "cytoscape needs to allow for multiple views of the same network for this to work")
A is a node (representing unmodified protein); central dot is a node (representing phosphorylated A) - every state is represented as a node. The PTM e.g. P is not a node, it is an annotation on the 'central' state node. The edge between A and its state is of type 'state of'. The set of all states is grouped to represent the set of all states of A. 
View: Constraint: the states always move together (would be like a template).

Binding two small molecules might have a different representation.


== Importance ==
## Describe whether this use case is critical and how frequently users would come across it.  Describe common work flows that might involve the use case (e.g., "this use case comes up regularly, on a weekly basis, whenever we want to analyze our protein superfamily networks").
Binding of small molecules is a basic reaction that occurs in most maps using Kohn notation.

== Variations ==
Common molecules that are used include:
 * Ac: Acetyl
 * Me: Methyl
 * OH: Hydroxy
 * P: Phosphate
 * Ub: Ubiquitin

If the protein in the covalently bound state is used in a subsequent reaction, a dot is placed on the line, and that is used to anchor the edges for the subsequent reactions. (See ../CompoundBinding)

{{attachment:covalentbinding3_061115_dwk.png}}

Unlike proteins, which appear only once on a particular map, for small molecules a copy of the icon appears each time it is involved in a reaction.
 
{{attachment:covalentbinding4_061115_dwk.png}}

In the past, a different notation for covalent binding was used.  The current notation better communicates the notion that the bond is symmetrical.  This legacy notation does not need to be supported:

{{attachment:covalentbinding5_061115_dwk.png}}

== Other Examples ==
## List other applications or relevant examples outside of Cytoscape that provide some or all of the desired functionality (e.g., "You can do this using the group function in PowerPoint").

== Comments ==
Shared ../MimEditorUseCaseComments

The BioPAX representation of this reaction could be a Biochemical Reaction object (e.g. Biochemical Reaction object with Interaction-Type = "phosphorylation", Participants = AP,A,P, Left = A,P, and Right = AP, where A, AP and P are physicalEntities.  Binding two small molecules might have a different representation.

----
AllanKuchinsky - 2007-01-27 14:22:11

From the 2006 Cytoscape Retreat notes:
Model: In the cases above, A is a node (representing unmodified protein); central dot is a node (represented modified A) - every state is represented as a node. The PTM e.g. P is not a node, it is an annotation on the 'central' state node. The edge between A and its state is of type 'state of'. The set of all states is grouped to represent the set of all states of A. 
View: Constraint: the states always move together (would be like a template)