lab42c.net

# Created by BioNetGen 2.1.7
substanceUnits("Number");
begin parameters
    1 RT 100 # Constant
    2 AT 1000 # Constant
    3 K2 0.1 # Constant
    4 K1 5e-5 # Constant
    5 c 1 # Constant
    6 LT 10000 # ConstantExpression
    7 km1 0.01 # Constant
    8 km2 0.01 # Constant
    9 kp1 5e-07 # ConstantExpression
   10 kp2 0.001 # ConstantExpression
   11 kph 1 # Constant
   12 kdph 0.1 # Constant
   13 KA 10 # Constant
   14 kda 0.1 # Constant
   15 ka 1 # ConstantExpression
end parameters
begin molecule types
  1 A(r)
  2 L(r1,r2)
  3 R(l1~U~P)
end molecule types 
begin observables
    1 Molecules phosporilated R(l1~P!?)
end observables
begin species
    1 L(r1,r2)                          LT
    2 R(l1~U)                           RT
    3 A(r)                              AT
    4 L(r1!1,r2).R(l1~U!1)              0
    5 L(r1!1,r2!2).R(l1~U!1).R(l1~U!2)  0
    6 L(r1!1,r2).R(l1~P!1)              0
    7 R(l1~P)                           0
    8 L(r1!1,r2!2).R(l1~P!1).R(l1~U!2)  0
    9 L(r1!1,r2!2).R(l1~P!2).R(l1~U!1)  0
   10 L(r1!1,r2!2).R(l1~P!1).R(l1~P!2)  0
   11 A(r!1).R(l1~P!1)                  0
   12 A(r!1).R(l1~U!1)                  0
end species
begin reaction rules
Rule1: \
  L(r1,r2) + R(l1) <-> R(l1!1).L(r1!1,r2) kp1, km1
# Bind(0.0.0,0.1.0)
# Reverse
# Unbind(0.0.0,0.1.0)
Rule2: \
  L(r1!+,r2) + R(l1) <-> L(r1!+,r2!1).R(l1!1) kp2, km2
# Bind(0.0.1,0.1.0)
# Reverse
# Unbind(0.0.1,0.1.0)
Rule3: \
  R(l1~U!+) -> R(l1~P!+) kph
# StateChange(0.0.0,U->P)
Rule4: \
  R(l1~P!?) -> R(l1~U!?) kdph
# StateChange(0.0.0,P->U)
Rule5: \
  R(l1~P) + A(r) <-> R(l1~P!1).A(r!1) ka, kda
# Bind(0.0.0,0.1.0)
# Reverse
# Unbind(0.0.0,0.1.0)
end reaction rules
begin reactions
    1 1,2 4 kp1 #Rule1
    2 4 1,2 km1 #Rule1r
    3 2,4 5 kp2 #Rule2
    4 4 6 kph #Rule3
    5 6 1,7 km1 #Rule1r
    6 2,6 8 kp2 #Rule2
    7 5 2,4 km2 #Rule2r
    8 5 8 kph #Rule3
    9 5 9 kph #Rule3
   10 6 4 kdph #Rule4
   11 1,7 6 kp1 #Rule1
   12 4,7 9 kp2 #Rule2
   13 6,7 10 kp2 #Rule2
   14 8 2,6 km2 #Rule2r
   15 9 4,7 km2 #Rule2r
   16 8 10 kph #Rule3
   17 9 10 kph #Rule3
   18 7 2 kdph #Rule4
   19 8 5 kdph #Rule4
   20 9 5 kdph #Rule4
   21 3,7 11 ka #Rule5
   22 10 6,7 km2 #Rule2r
   23 10 9 kdph #Rule4
   24 10 8 kdph #Rule4
   25 11 12 kdph #Rule4
   26 11 3,7 kda #Rule5r
   27 12 11 kph #Rule3
end reactions
begin groups
    1 phosporilated        6,7,8,9,2*10,11
end groups