Use Case Name : ../AsymmetricBinding

For Feature : MIMEditor

Editors: DavidKane

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A user wants to describe the possibility that a protein binds to another and contributes a peptide that binds to a receptor site or pocket on another protein.

Step-by-Step User Action

  1. User specifies a protein to be involved in the interaction as a contributor
  2. User specifies another protein to be involved in the reaction as a receptor
  3. User specifies that there is an asymmetric binding reaction between the two
  4. User optionally specifies the evidence for this reaction

Visual Aides

The Kohn notation for this reaction is the following:


An example using this notation follows:


Requirements for Cytoscape

This would be modeled similarly to a ../NonCovalentBinding, i.e. with a group, but with a specific edge type. The barbed arrow would require custom rendering.


This notation is fairly rare and is not as important as the other use cases.


If the bound proteins are 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)


Other Examples


Shared ../MimEditorUseCaseComments

The BioPAX representation of this binding could be a Conversion Object, i.e. with Participants = A,B, AB, Left = A,B, Right=AB, where A and B are Proteins, but AB is a complex with components A and B). It is not clear how to differentiate simple binding from asymmetric binding in BioPAX.

Molecular_Interaction_Maps/AsymmetricBinding (last edited 2009-02-12 01:04:04 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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