# allostery.txt
# This model demonstrates the use of allostery in a model using an
# allosteric-class.  Receptor molecules bind to Ligand in a standard
# association reaction.  Receptor molecules can also bind to
# SecondMessengers when their secondary_site is in the Active form.  A
# rule in the allosteric-classes section specifies Receptor.Ligand
# subcomplexes change Receptor's secondary_site from Occluded to
# Active.

graphics opengl_good
graphic_delay 100

dim 3

max_species 100


start_rules
===== Molecules ======================
      Ligand, mass = 100.0;
      Receptor(ligand_site, secondary_site {Occluded, Active}), mass = 10000.0;
      SecondMessenger( site), mass = 10000.0;

===== Association-Reactions =========	

      Receptor(ligand_site) + Ligand -> Receptor(ligand_site!1).Ligand(!1),
      	      kon = 500,
	      koff = 0.0;

      Receptor(secondary_site) + SecondMessenger( site ) -> Receptor(secondary_site!1).SecondMessenger( site!1 ),
             kon = 0.0,
	     koff = 10000,

	     Receptor(secondary_site {Active} ) + SecondMessenger( site ) -> Receptor(secondary_site!1).SecondMessenger( site!1 ),
	         kon = 500.0,
		 koff = 0.0;

=== Allosteric-Classes ================
    Receptor( secondary_site { Active <- *}, ligand_site!1).Ligand(!1);

===== Explicit-Species ===============
      Receptor(ligand_site!1).Ligand(!1),
	name = ReceptorBoundLigand;

	Receptor(ligand_site!2, secondary_site!1).SecondMessenger(site!1).Ligand(!2),
		name = ReceptorBoundMessenger;

end_rules

species Receptor Ligand SecondMessenger ReceptorBoundLigand ReceptorBoundMessenger

difc Receptor 100.0
difc Ligand 100.0
difc SecondMessenger 100.0
difc ReceptorBoundLigand 100.0
difc ReceptorBoundMessenger 100.0

max_mol 10000;

color Receptor 0 1 0
color Ligand 1 0 0
color SecondMessenger 0 0 1

color ReceptorBoundLigand 1 1 0 
color ReceptorBoundMessenger 0 1 1


display_size ReceptorBoundLigand 5.0
display_size ReceptorBoundMessenger 10.0

time_start 0
time_stop 100
time_step 0.01

boundaries 0 0 100 r
boundaries 1 0 100 r
boundaries 2 0 100 r


mol 100 Receptor 90 90 90
mol 100 SecondMessenger 50 50 50 
mol 100 Ligand 10 10 10

cmd b pause

end_file


color