12. Complex association
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12. Complex association

12.1. Complex association editing window

  1. The window for complex association editing

  2. "Add Complex" side window section

    This window section is similar to the "Complexes" side window section in the complex species editing window, but this window section does not contain the "New", "View" and "Delete" buttons. If the current complex association editing window only has one complex loaded, double clicking an item in the list of this complex side window section or clicking the "Add" button will load the second complex as a binding partner for the association. If the clicked item is a complex species, all states of molecule component tags and statuses of binding sites not involving in-complex binding are initialized as default "Don't Care".

  3. "Add Molecule" side window section

    If the "Automatically Create Single Molecule Complex Species When Saving New Molecule " is unchecked, this tab window is enabled to add a molecule as a single molecule complex for building a rule of complex association.

    Similar to the "Molecules" side window section in the complex species editing window, this window section displays a list of molecules in the current model.

    If the single molecule complex species corresponding to the selected molecule has not yet been defined, a message window will display a warning message.

    If there is no defined complex species matching the single molecule, after clicking "OK", the complex 2 window displays a page to define a new complex species. The button "Save As New Complex Species" is highlighted in orange to remind the user that this should be done next.

  4. The graphical layout window section for the complex interaction

    This window section displays the graphical layout of the complexes and the interaction linking the two complexes. If the interaction between the two complexes has not been set up yet, the user can draw the interaction between a pair of binding sites of different complexes. If the modeler application detects that the same interaction has been defined before, all data of the predefined complex association will be loaded.

    The user can highlight a complex by double clicking a binding site or a molecule component. Once the complex is highlighted, it can be rotated by clicking the "Rotate +90o" or the "Rotate -90o" button, or flipped by clicking the "Flip" button. If a binding site interaction between the two complexes has already been defined, the user can remove the interaction by clicking the "Reset Interaction" button".

    The window may also have "Center" button, see details in preference section.

  5. The graphical layout window section for the result complex

    This window section displays the graphical layout of the result complex.

    The window may also have "Center" button, see details in preference section.

  6. The window section for "Source Complex 1"

    The fields and the usage of this window section are the same as for the "Source" complex in the transformation editing window. This window section is for the complex 1 in the association.

  7. The window section for "Source Complex 2"

    This window section has all the fields described in the "Source" complex in the transformation editing window. This window section is for source complex 2 in an association.

    This window section has another button "Reset". When this button is clicked, the modeler application clears the information and graphical layouts of "Result Complex", "Source Complex 2" and the complex interaction (if already defined).

    One special case for source complex 2 has been discussed in the section about the "Add Molecule" side window section.

  8. The window section for "Result complex"

    The fields and the usage of this window section are the same as for the "Source" complex in the transformation editing window. This window section is for the result complex in the association.

    When the result complex has not been defined yet, the result complex field looks as shown below:

    The user should click the "Define Result Complex Species" button:

    Click the "Save and Back" button after defining the complex species. If you want to cancel the definition of a new complex species, simply click the "back" button.

  9. Association Properties

    • Assoc Name

      The modeler gives a default association short name and the user may modify it.

    • Assoc Rate and Rate Unit

      The association rate field expects a number format. The rate unit depends on the type of the association. When the association is 2D, the rate unit is " microns 2 /s ". When the association is 3D, the rate unit is " /mol s ". When the association is "Intra Complex", the unit is " /s ".

    • Annotation

      Free text field for the user to provide annotation.

    • Orientation

      Some molecular interactions can occur between molecules (receptors) located in the same membrane and, with typically different characteristics, between molecules facing each other in opposite adjacent membranes of two cells or of another region of the same cell folding back onto its own membrane. The modeler application permits specifying different rates depending on this relative orientation of the interaction complexes. The user can choose from three tags: "No orientation", "trans-binding" and "cis-binding". This orientation specification will be implemented by the simulator application building the local interaction networks in the simulated cellular morphology.

  10. Control buttons.

    • "Save" button

      When this button is clicked, a saving request is sent to the modeler application. The moder application will first check the completeness of the data for the association. If the check is passed, the modeler application saves the current association data to the model file.

      The modeler application will dectect if there is any conflicting data. If the modeler application finds an conflicting situation, a message window prompts the user to decide how to handle the conflict.

      • Conflicting case 1: the current association has orientation conflicting with saved association rule(s).

        "No orientation" conflicts to "trans-binding" or "cis-binding", and verse visa.

        The user may click "No" to keep the model file unchanged, or click "Yes" to save anyway.

        Note

        Note that reactions that have no specific orientation defined by the user will be applied to all complexes matching the structural properties and states of the complex (pattern) in the reaction definition. If, additionally, reactions for the same (or equivalent) complexes have been defined that depend on a particular orientation (cis or trans) of the reacting complex(es) these reactions will be applied parallel to the ones without orientation but will not replace those.

      • Conflicting case 2: a complex has been changed for an existing association and the association with the changed complex has not been defined yet.

      • Conflicting case 3: a complex has been changed for an existing association and the association with changed complex has been defined.

      • Conflicting case 4: the current association is created as new, but it has been defined before.

    • "Back" button

      When this button is clicked, the modeler application goes back to the previous window.

    • "Delete" button

      The modeler application will delete the association record with the Assoc ID of the current association and then go back to the previous window.

    • "Create Reverse Dissociation" button

      A convenient way to initialize creating a dissociation rule. Go to the dissociation editing window and reverse the association source and result complexes.

      This button only appears when displaying an existing association rule (saved or loaded).

  11. "Display Molecule Mapping"

    If this checkbox is checked, the both graphical layout window sections will show the indices of the molecules in the result complex so the user can see the molecule mapping relationship. Otherwise, the mapping index ids are hidden.

12.2. Creating/editing a complex association

  1. Creating a new association

    The user can create a new association using the "New" button in the "Relations" in either the complex species editing window or the complex editing window.

    If the association is created from a complex species, the modeler application will set "Don't care" as the default value for all molecule component tags and binding site statuses to initialize a complex and the user can make changes afterwards. The pair of binding sites involved in the association assume an "Unbound" state in the two molecules (on the left, before binding) when the association line is defined.

  2. Load an existing association

    An existing association can be loaded:

  3. Edit

    The fields which can be edited include:

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11. Transformation Home 13. Complex dissociation