Molecular_Interaction_Maps/EnzymaticStimulation

TableOfContents([2])

Summary

A user wants specify that a species is an enzyme that stimulates a reaction

Step-by-Step User Action

1. User specifies a species to be the enzymatic stimulator
2. User specifies a reaction to be stimulated
3. User specifies that there is a stimulation relationship
4. User optionally specifies the evidence for the relationship

Visual Aides

The Kohn notation for enzymatic stimulation is the following:

An example using this notation follows:

Requirements for Cytoscape

Assuming that this can use the same approach that is used for self:Inhibition, it could be modeled as a Hyperedge containing node1: C (hyperedge attribute: enzymatic stimulation), node2: A, node3: B

View: Use case for hyperedge view

Importance

TBD

Other Examples

Comments

Shared MimEditorUseCaseComments

This is a special case of a ProcessStimulation. The enzyme binds to the complex as part of the reaction, and is unmodified after the reaction.

This could be modeled in BioPAX as a Catalysis object (e.g. Catalysis object with participants = a physicalInteraction object and a enzyme A, Controlled = the physicalInteraction object, Controller=A, Control-Type = Activation, and Direction = IRREVERSIBLE-LEFT-TO-RIGHT)

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