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Name - Pin1_2domain(diffKds)_w_Bivalentligand(diffKds)

BioModel ID - 116704767

Reaction Diagram

Physiology

Universal ID's	Text Annotations

Reactions See in Dashboard
Reaction	Name Structure	Kinetics	Depiction
Pin1A_Pin1BivAB	r4 c0	MassAction	Pin1A_Pin1BivAB
		reaction rate (J): ((Kf * Pin1A_) - (Kr * Pin1BivAB))[uM.s-1] forward rate constant (Kf): 100.0[s-1] reverse rate constant (Kr): 18.5[s-1]
Pin1+LigPin1_A	r0 c0	MassAction	Pin1+LigPin1_A
		reaction rate (J): (((Kf * Pin1) * Lig) - (Kr * Pin1_A))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 68100.0[s-1]
Pin1+LigPin1B_	r1 c0	MassAction	Pin1+LigPin1B_
		reaction rate (J): (((Kf * Pin1) * Lig) - (Kr * Pin1B_))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 23100.0[s-1]
Pin1_APin1BivBA	r6 c0	MassAction	Pin1_APin1BivBA
		reaction rate (J): ((Kf * Pin1_A) - (Kr * Pin1BivBA))[uM.s-1] forward rate constant (Kf): 100.0[s-1] reverse rate constant (Kr): 23.1[s-1]
Pin1B_Pin1BivBA	r7 c0	MassAction	Pin1B_Pin1BivBA
		reaction rate (J): ((Kf * Pin1B_) - (Kr * Pin1BivBA))[uM.s-1] forward rate constant (Kf): 100.0[s-1] reverse rate constant (Kr): 68.1[s-1]
Pin1_A+LigPin1AA	r8 c0	MassAction	Pin1_A+LigPin1AA
		reaction rate (J): (((Kf * Pin1_A) * Lig) - (Kr * Pin1AA))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 21500.0[s-1]
Lig+Pin1A_Pin1AA	r9 c0	MassAction	Lig+Pin1A_Pin1AA
		reaction rate (J): (((Kf * Lig) * Pin1A_) - (Kr * Pin1AA))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 68100.0[s-1]
Pin1B_+LigPin1BB	r12 c0	MassAction	Pin1B_+LigPin1BB
		reaction rate (J): (((Kf * Pin1B_) * Lig) - (Kr * Pin1BB))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 18500.0[s-1]
Pin1_B+LigPin1BB	r13 c0	MassAction	Pin1_B+LigPin1BB
		reaction rate (J): (((Kf * Pin1_B) * Lig) - (Kr * Pin1BB))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 23100.0[s-1]
Pin1_A+LigPin1BA	r16 c0	MassAction	Pin1_A+LigPin1BA
		reaction rate (J): (((Kf * Pin1_A) * Lig) - (Kr * Pin1BA))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 23100.0[s-1]
Pin1B_+LigPin1BA	r17 c0	MassAction	Pin1B_+LigPin1BA
		reaction rate (J): (((Kf * Pin1B_) * Lig) - (Kr * Pin1BA))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 68100.0[s-1]
Pin1_BPin1BivAB	r5 c0	MassAction	Pin1_BPin1BivAB
		reaction rate (J): ((Kf * Pin1_B) - (Kr * Pin1BivAB))[uM.s-1] forward rate constant (Kf): 100.0[s-1] reverse rate constant (Kr): 21.5[s-1]
Pin1_B+LigPin1AB	r20 c0	MassAction	Pin1_B+LigPin1AB
		reaction rate (J): (((Kf * Pin1_B) * Lig) - (Kr * Pin1AB))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 21500.0[s-1]
Pin1A_+LigPin1AB	r21 c0	MassAction	Pin1A_+LigPin1AB
		reaction rate (J): (((Kf * Pin1A_) * Lig) - (Kr * Pin1AB))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 18500.0[s-1]
Pin1+LigPin1A_	r2 c0	MassAction	Pin1+LigPin1A_
		reaction rate (J): (((Kf * Pin1) * Lig) - (Kr * Pin1A_))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 21500.0[s-1]
Pin1+LigPin1_B	r3 c0	MassAction	Pin1+LigPin1_B
		reaction rate (J): (((Kf * Pin1) * Lig) - (Kr * Pin1_B))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 18500.0[s-1]
Pin1+Pin1B_Pin1B_Pin1A_	r10 c0	MassAction	Pin1+Pin1B_Pin1B_Pin1A_
		reaction rate (J): (((Kf * Pin1) * Pin1B_) - (Kr * Pin1B_Pin1A_))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 21500.0[s-1]
Pin1+Pin1_BPin1_BPin1_A	r15 c0	MassAction	Pin1+Pin1_BPin1_BPin1_A
		reaction rate (J): (((Kf * Pin1) * Pin1_B) - (Kr * Pin1_BPin1_A))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 68100.0[s-1]
Pin1+Pin1A_Pin1A_Pin1_B	r18 c0	MassAction	Pin1+Pin1A_Pin1A_Pin1_B
		reaction rate (J): (((Kf * Pin1) * Pin1A_) - (Kr * Pin1A_Pin1_B))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 18500.0[s-1]
Pin1+Pin1_APin1_APin1B_	r22 c0	MassAction	Pin1+Pin1_APin1_APin1B_
		reaction rate (J): (((Kf * Pin1) * Pin1_A) - (Kr * Pin1_APin1B_))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 23100.0[s-1]
Pin1_B+Pin1Pin1A_Pin1_B	r24 c0	MassAction	Pin1_B+Pin1Pin1A_Pin1_B
		reaction rate (J): (((Kf * Pin1_B) * Pin1) - (Kr * Pin1A_Pin1_B))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 21500.0[s-1]
Pin1_A+Pin1Pin1_BPin1_A	r14 c0	MassAction	Pin1_A+Pin1Pin1_BPin1_A
		reaction rate (J): (((Kf * Pin1_A) * Pin1) - (Kr * Pin1_BPin1_A))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 18500.0[s-1]
Pin1B_+Pin1Pin1_APin1B_	r23 c0	MassAction	Pin1B_+Pin1Pin1_APin1B_
		reaction rate (J): (((Kf * Pin1B_) * Pin1) - (Kr * Pin1_APin1B_))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 68100.0[s-1]
Pin1A_+Pin1Pin1B_Pin1A_	r11 c0	MassAction	Pin1A_+Pin1Pin1B_Pin1A_
		reaction rate (J): (((Kf * Pin1A_) * Pin1) - (Kr * Pin1B_Pin1A_))[uM.s-1] forward rate constant (Kf): 100.0[s-1.uM-1] reverse rate constant (Kr): 23100.0[s-1]

Structures See in Dashboard
Name	Type Electrical (Membrane Polarity)
c0	Compartment (+) (-)

Species See in Dashboard
Name	Structure	BioNetGen Definition
Pin1AA	c0

Pin1BB	c0

Pin1AB	c0

Pin1BA	c0

Lig	c0

Pin1	c0

Pin1_B	c0

Pin1BivAB	c0

Pin1A_	c0

Pin1_A	c0

Pin1B_	c0

Pin1BivBA	c0

Pin1B_Pin1A_	c0

Pin1_APin1B_	c0

Pin1A_Pin1_B	c0

Pin1_BPin1_A	c0

Molecules See in Dashboard
Name	Text Annotations	BioNetGen Definition

Observables See in Dashboard
Name	Type Count	BioNetGen Definition

Applications

Applications See in Dashboard
Name	Math Type	Annotation
Application0	Deterministic (ODE) Compartmental

Application - Application0

Specifications(Species) - Application0 See in Dashboard
Species	Initial Condition	Diffusion Constant
Pin1AA	0.0 [uM]	0.0 [um2/s]
Pin1BB	0.0 [uM]	0.0 [um2/s]
Pin1AB	0.0 [uM]	0.0 [um2/s]
Pin1BA	0.0 [uM]	0.0 [um2/s]
Lig	44.0 [uM]	0.0 [um2/s]
Pin1	196.0 [uM]	0.0 [um2/s]
Pin1_B	0.0 [uM]	0.0 [um2/s]
Pin1BivAB	0.0 [uM]	0.0 [um2/s]
Pin1A_	0.0 [uM]	0.0 [um2/s]
Pin1_A	0.0 [uM]	0.0 [um2/s]
Pin1B_	0.0 [uM]	0.0 [um2/s]
Pin1BivBA	0.0 [uM]	0.0 [um2/s]
Pin1B_Pin1A_	0.0 [uM]	0.0 [um2/s]
Pin1_APin1B_	0.0 [uM]	0.0 [um2/s]
Pin1A_Pin1_B	0.0 [uM]	0.0 [um2/s]
Pin1_BPin1_A	0.0 [uM]	0.0 [um2/s]

Specifications(Reaction) - Application0 See in Dashboard
Name	Reaction Mapping
r4	included
r0	included
r1	included
r6	included
r7	included
r8	included
r9	included
r12	included
r13	included
r16	included
r17	included
r5	included
r20	included
r21	included
r2	included
r3	included
r10	included
r15	included
r18	included
r22	included
r24	included
r14	included
r23	included
r11	included

Simulations - Application0 See in Dashboard
Name	End Time	Output Options
Pin1=196uM,IKpS163173=44uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
Pin1=212uM,IKpS163173=2640uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
from2BR_prot_Pin1=196uM,IKpS163173=44uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
from2BR_prot_Pin1=201uM,IKpS163173=55uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
from2BR_prot_Pin1=206uM,IKpS163173=82uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
from2BR_prot_Pin1=224uM,IKpS163173=165uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
from2BR_prot_Pin1=237uM,IKpS163173=330uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
from2BR_prot_Pin1=250uM,IKpS163173=660uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
from2BR_prot_Pin1=244uM,IKpS163173=1320uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
from2BR_prot_Pin1=212uM,IKpS163173=2640uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
from2brprot Pin1=196uM,IKpS131144=44uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_Pin1=250uM,IKpS163173=37uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_Pin1=250uM,IKpS163173=73uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_Pin1=250uM,IKpS163173=147uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_Pin1=250uM,IKpS163173=293uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_Pin1=250uM,IKpS163173=587uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_Pin1=250uM,IKpS163173=1174uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_Pin1=250uM,IKpS163173=2347uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_nitrogen_Pin1=250uM,IKpS163173=37uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_nitrogen_Pin1=250uM,IKpS163173=73uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_nitrogen_Pin1=250uM,IKpS163173=147uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_nitrogen_Pin1=250uM,IKpS163173=293uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_nitrogen_Pin1=250uM,IKpS163173=587uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_nitrogen_Pin1=250uM,IKpS163173=1174uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
131144_2br_nitrogen_Pin1=250uM,IKpS163173=2347uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
testw1branch#_2BR_prot_Pin1=196uM,IKpS163173=44uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
testw1branch#_2BR_prot(lessbr2)_Pin1=196uM,IKpS163173=44uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
IRAK1B_2BR_prot_Pin1=13uM,IKpS163173=519uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
IRAK1B_2BR_prot_Pin1=27uM,IKpS163173=519uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
IRAK1B_2BR_prot_Pin1=53uM,IKpS163173=518uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
IRAK1B_2BR_prot_Pin1=106uM,IKpS163173=516uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
IRAK1B_2BR_prot_Pin1=213uM,IKpS163173=511uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
IRAK1B_2BR_prot_Pin1=425uM,IKpS163173=503uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
IRAK1B_2BR_prot_Pin1=850uM,IKpS163173=485uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=37uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=73uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=147uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=293uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=587uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=1174uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_prot_Pin1=250uM,IKpS131144=2347uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=37uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=73uM	10.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=147uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=293uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=587uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=1174uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Octrefit_nit_Pin1=250uM,IKpS131144=2347uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel6373_refitOct_prot_Pin1=196uM,IKpS163173=44uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel6373_refitOct_prot_Pin1=201uM,IKpS163173=55uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel6373_refitOct_prot_Pin1=206uM,IKpS163173=82uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel6373_refitOct_prot_Pin1=224uM,IKpS163173=165uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel6373_refitOct_prot_Pin1=237uM,IKpS163173=330uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel6373_refitOct_prot_Pin1=250uM,IKpS163173=660uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel6373_refitOct_prot_Pin1=244uM,IKpS163173=1320uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel6373_refitOct_prot_Pin1=212uM,IKpS163173=2640uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitNov_Ni_Pin1=196uM,IKpS163173=44uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitOct_Ni_Pin1=201uM,IKpS163173=55uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitOct_Ni_Pin1=206uM,IKpS163173=82uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitOct_Ni_Pin1=224uM,IKpS163173=165uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitOct_Ni_Pin1=237uM,IKpS163173=330uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitOct_Ni_Pin1=250uM,IKpS163173=660uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitOct_Ni_Pin1=244uM,IKpS163173=1320uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitOct_Ni_Pin1=212uM,IKpS163173=2640uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitNov_Ni_Pin1=201uM,IKpS163173=55uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitNov_Ni_Pin1=206uM,IKpS163173=82uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitNov_Ni_Pin1=224uM,IKpS163173=165uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitNov_Ni_Pin1=237uM,IKpS163173=330uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitNov_Ni_Pin1=250uM,IKpS163173=660uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitNov_Ni_Pin1=244uM,IKpS163173=1320uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_refitNov_Ni_Pin1=212uM,IKpS163173=2640uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=37uM	10.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=147uM	10.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=293uM	10.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=587uM	10.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=1170uM	10.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_Novrefit_nit_Pin1=250uM,IKpS131144=2347uM	10.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_testpopgrab_Ni_Pin1=201uM,IKpS163173=55uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_testpopcalc_Ni_Pin1=201uM,IKpS163173=55uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_testscalekeq_Ni_Pin1=201uM,IKpS163173=55uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000
2brmodel_testnewscalekeq_Ni_Pin1=201uM,IKpS163173=55uM	1.0 [s]	KeepEvery 1 KeepAtMost 1000

Geometry non-spatial120107596 See in Dashboard
(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0[um])
Dimension	Type	Subdomain	Adjacent Subvolumes	Size	Mapped Compartment
	Compartmental	Compartment			c0

Global Parameters

Global Parameters See in Dashboard
Name	Expression