Physiology
Reaction Diagram
Cross-References
Annotations
Reactions
| Reactions | Name | Structure | Kinetics | Depiction |
|---|---|---|---|---|
| Raf1+GTP_RasRas_Raf1 | Ras_Raf1_bind | pm | MassAction | |
| Ras_BRaf+Ras_Raf1Ras_BRaf_Raf1_tetramer | BRaf_Raf1_bind | pm | MassAction | |
| Ras_BRaf_Raf1_tetramerRas_BRaf_pRaf1_tetramer | BRaf_Raf1_phosph | pm | MassAction | |
| Ras_pRaf1pRaf1+GTP_Ras | Ras_pRaf1_unbind | pm | MassAction | |
| BRaf+GTP_RasRas_BRaf | Ras_BRaf_bind | pm | MassAction | |
| Ras_pRaf1+Ras_Raf1Ras_pRaf1_Raf1_tetramer | pRaf1_Raf1_bind | pm | MassAction | |
| Ras_pRaf1_Raf1_tetramerRas_pRaf1_tetramer | pRaf1_Raf1_phosph | pm | MassAction | |
| sorafenib+Raf1iRaf1 | sorafenib_Raf1_bind_cyt | cytoplasm | MassAction | |
| iRaf1+GTP_RasRas_iRaf1 | Ras_iRaf1_bind | pm | MassAction | |
| Ras_iRaf1Ras_iRaf1_tetramer | iRaf1_iRaf1_bind | pm | MassAction | |
| Ras_BRaf+Ras_iRaf1Ras_Braf_iRaf1_tetramer | BRaf_iRaf1_bind | pm | MassAction | |
| pRaf1Raf1 | pRaf1_dephosph | cytoplasm | MassAction | |
| Ras_pRaf1_tetramerRas_pRaf1 | pRaf1_pRaf1_unbind | pm | MassAction | |
| Ras_BRaf_pRaf1_tetramerRas_BRaf+Ras_pRaf1 | BRaf_pRaf1_unbind | pm | MassAction | |
| sorafenib+BRafiBRaf | sorafenib_BRaf_bind_cyt | cytoplasm | MassAction | |
| MEKpMEK | MEK_p | cytoplasm | MassAction | |
| pMEKMEK | MEK_dp | cytoplasm | MassAction | |
| ERKpERK | ERK_p | cytoplasm | MassAction | |
| pERKERK | ERK_dp | cytoplasm | MassAction | |
| iBRafRas_iBRaf | Ras_iBRaf_b | pm | MassAction | |
| Ras_iBRafiBRaf_dimer | iBRaf_dim | pm | MassAction | |
| Ras_Raf1+Ras_iBRafRas_Raf1_iBRaf_tetramer | iBRaf_Raf1_bind | pm | MassAction | |
| Ras_Raf1_iBRaf_tetramerRas_pRaf1_iBRaf_tetramer | Raf1_iBRaf_p | pm | MassAction | |
| Ras_pRaf1_iBRaf_tetramerRas_iBRaf+Ras_pRaf1 | pRaf1_iBRaf_ub | pm | MassAction | |
| Ras_BRafBRaf_dimer | BRaf_dim | pm | MassAction | |
| Ras_pRaf1Ras_Raf1 | Ras_pRaf1_dp | pm | MassAction | |
| Ras_Raf1Ras_nfpRaf1 | Ras_Raf1_nfp | pm | MassAction | |
| Ras_nfpRaf1GTP_Ras+nfpRaf1 | nfpRaf1_ub | pm | MassAction | |
| nfpRaf1Raf1 | nfpRaf1_dp | cytoplasm | MassAction | |
| Ras_BRafRas_nfpBRaf | BRaf_nfp | pm | MassAction | |
| Ras_nfpBRafGTP_Ras+nfpBRaf | nfpBRaf_ub | pm | MassAction | |
| nfpBRafBRaf | nfpBRaf_dp | cytoplasm | MassAction | |
| Ras_iBRaf+Ras_BRafBRaf_iBRaf_dimer | BRaf_iBRaf_dim | pm | MassAction | |
| Ras_iRaf1Ras_nfpiRaf1 | Ras_iRaf_nfp | pm | MassAction | |
| Ras_nfpiRaf1nfpiRaf1+GTP_Ras | nfpiRaf1_ub | pm | MassAction | |
| nfpiRaf1iRaf1 | nfpiRaf_dp | cytoplasm | MassAction | |
| Ras_iBRafRas_nfpiBRaf | Ras_iBRaf_nfp | pm | MassAction | |
| Ras_nfpiBRafnfpiBRaf+GTP_Ras | nfpiBRaf_ub | pm | MassAction | |
| nfpiBRafiBRaf | nfpiBRaf_dp | cytoplasm | MassAction | |
| Ras_iRaf1+Ras_iBRafRas_iRaf1_iBRaf1_tetramer | iRaf_iBRaf_dim | pm | MassAction |
Ras_Raf1_bind Universal ID's
Ras_Raf1_bind Text Annotations
BRaf_Raf1_bind Universal ID's
BRaf_Raf1_bind Text Annotations
BRaf_Raf1_phosph Universal ID's
BRaf_Raf1_phosph Text Annotations
Ras_pRaf1_unbind Universal ID's
Ras_pRaf1_unbind Text Annotations
Ras_BRaf_bind Universal ID's
Ras_BRaf_bind Text Annotations
pRaf1_Raf1_bind Universal ID's
pRaf1_Raf1_bind Text Annotations
pRaf1_Raf1_phosph Universal ID's
pRaf1_Raf1_phosph Text Annotations
sorafenib_Raf1_bind_cyt Universal ID's
sorafenib_Raf1_bind_cyt Text Annotations
Ras_iRaf1_bind Universal ID's
Ras_iRaf1_bind Text Annotations
iRaf1_iRaf1_bind Universal ID's
iRaf1_iRaf1_bind Text Annotations
BRaf_iRaf1_bind Universal ID's
BRaf_iRaf1_bind Text Annotations
pRaf1_dephosph Universal ID's
pRaf1_dephosph Text Annotations
pRaf1_pRaf1_unbind Universal ID's
pRaf1_pRaf1_unbind Text Annotations
BRaf_pRaf1_unbind Universal ID's
BRaf_pRaf1_unbind Text Annotations
sorafenib_BRaf_bind_cyt Universal ID's
sorafenib_BRaf_bind_cyt Text Annotations
MEK_p Universal ID's
MEK_p Text Annotations
MEK_dp Universal ID's
MEK_dp Text Annotations
ERK_p Universal ID's
ERK_p Text Annotations
ERK_dp Universal ID's
ERK_dp Text Annotations
Ras_iBRaf_b Universal ID's
Ras_iBRaf_b Text Annotations
iBRaf_dim Universal ID's
iBRaf_dim Text Annotations
iBRaf_Raf1_bind Universal ID's
iBRaf_Raf1_bind Text Annotations
Raf1_iBRaf_p Universal ID's
Raf1_iBRaf_p Text Annotations
pRaf1_iBRaf_ub Universal ID's
pRaf1_iBRaf_ub Text Annotations
BRaf_dim Universal ID's
BRaf_dim Text Annotations
Ras_pRaf1_dp Universal ID's
Ras_pRaf1_dp Text Annotations
Ras_Raf1_nfp Universal ID's
Ras_Raf1_nfp Text Annotations
nfpRaf1_ub Universal ID's
nfpRaf1_ub Text Annotations
nfpRaf1_dp Universal ID's
nfpRaf1_dp Text Annotations
BRaf_nfp Universal ID's
BRaf_nfp Text Annotations
nfpBRaf_ub Universal ID's
nfpBRaf_ub Text Annotations
nfpBRaf_dp Universal ID's
nfpBRaf_dp Text Annotations
BRaf_iBRaf_dim Universal ID's
BRaf_iBRaf_dim Text Annotations
Ras_iRaf_nfp Universal ID's
Ras_iRaf_nfp Text Annotations
nfpiRaf1_ub Universal ID's
nfpiRaf1_ub Text Annotations
nfpiRaf_dp Universal ID's
nfpiRaf_dp Text Annotations
Ras_iBRaf_nfp Universal ID's
Ras_iBRaf_nfp Text Annotations
nfpiBRaf_ub Universal ID's
nfpiBRaf_ub Text Annotations
nfpiBRaf_dp Universal ID's
nfpiBRaf_dp Text Annotations
iRaf_iBRaf_dim Universal ID's
iRaf_iBRaf_dim Text Annotations
Expressions for Ras_Raf1_bind
reaction rate
J
(((Kf * Raf1) * GTP_Ras) - (Kr * Ras_Raf1)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kR1f [min-1.uM-1]
global
kR1f
1.84E-7 [molecules.min-1]
reverse rate constant
Kr
kR1r [min-1]
global
kR1r
0.212 [min-1]
Expressions for BRaf_Raf1_bind
reaction rate
J
(((Kf * Ras_BRaf) * Ras_Raf1) - (Kr * Ras_BRaf_Raf1_tetramer)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
reverse rate constant
Kr
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
Expressions for BRaf_Raf1_phosph
reaction rate
J
((Kf * Ras_BRaf_Raf1_tetramer) - (Kr * Ras_BRaf_pRaf1_tetramer)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kpR1 [min-1]
global
kpR1
186.0 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for Ras_pRaf1_unbind
reaction rate
J
((Kf * Ras_pRaf1) - ((Kr * pRaf1) * GTP_Ras)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kR1r [min-1]
global
kR1r
0.212 [min-1]
reverse rate constant
Kr
kR1f [min-1.uM-1]
global
kR1f
1.84E-7 [molecules.min-1]
Expressions for Ras_BRaf_bind
reaction rate
J
(((Kf * BRaf) * GTP_Ras) - (Kr * Ras_BRaf)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kBf [min-1.uM-1]
global
kBf
2.47E-7 [min-1.molecules-1]
global
B
3.6724 [tbd]
reverse rate constant
Kr
kBr [min-1]
global
kBr
0.0367 [min-1]
global
B
3.6724 [tbd]
Expressions for pRaf1_Raf1_bind
reaction rate
J
(((Kf * Ras_pRaf1) * Ras_Raf1) - (Kr * Ras_pRaf1_Raf1_tetramer)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
reverse rate constant
Kr
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
Expressions for pRaf1_Raf1_phosph
reaction rate
J
((Kf * Ras_pRaf1_Raf1_tetramer) - (Kr * Ras_pRaf1_tetramer)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kpR1 [min-1]
global
kpR1
186.0 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for sorafenib_Raf1_bind_cyt
reaction rate
J
(((Kf * sorafenib) * Raf1) - (Kr * iRaf1)) [uM.min-1]
forward rate constant
Kf
kSon [min-1.uM-1]
global
kSon
100000.0 [uM-1.min-1]
reverse rate constant
Kr
kSoff [min-1]
global
kSoff
420.0 [min-1]
Expressions for Ras_iRaf1_bind
reaction rate
J
(((Kf * iRaf1) * GTP_Ras) - (Kr * Ras_iRaf1)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kiR1f [min-1.uM-1]
global
kiR1f
1.84E-7 [min-1.molecules-1]
reverse rate constant
Kr
kiR1r [min-1]
global
kiR1r
0.212 [min-1]
Expressions for iRaf1_iRaf1_bind
reaction rate
J
((Kf * pow(Ras_iRaf1,2.0)) - (Kr * Ras_iRaf1_tetramer)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
reverse rate constant
Kr
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
Expressions for BRaf_iRaf1_bind
reaction rate
J
(((Kf * Ras_BRaf) * Ras_iRaf1) - (Kr * Ras_Braf_iRaf1_tetramer)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
reverse rate constant
Kr
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
Expressions for pRaf1_dephosph
reaction rate
J
((Kf * pRaf1) - (Kr * Raf1)) [uM.min-1]
forward rate constant
Kf
kdpR1 [min-1]
global
kdpR1
0.6 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for pRaf1_pRaf1_unbind
reaction rate
J
((Kf * Ras_pRaf1_tetramer) - (Kr * pow(Ras_pRaf1,2.0))) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
reverse rate constant
Kr
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
Expressions for BRaf_pRaf1_unbind
reaction rate
J
((Kf * Ras_BRaf_pRaf1_tetramer) - ((Kr * Ras_BRaf) * Ras_pRaf1)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
reverse rate constant
Kr
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
Expressions for sorafenib_BRaf_bind_cyt
reaction rate
J
(((Kf * sorafenib) * BRaf) - (Kr * iBRaf)) [uM.min-1]
global
B
3.6724 [tbd]
forward rate constant
Kf
kSon [min-1.uM-1]
global
kSon
100000.0 [uM-1.min-1]
reverse rate constant
Kr
kSoff [min-1]
global
kSoff
420.0 [min-1]
Expressions for MEK_p
reaction rate
J
((Kf * MEK) - (Kr * pMEK)) [uM.min-1]
forward rate constant
Kf
(kMEKp * active_Raf) [min-1]
global
kMEKp
6.0E-6 [molecules-1.min-1]
global
active_Raf
((2.0 * BRaf_dimer) + Ras_BRaf_Raf1_tetramer + (2.0 * Ras_BRaf_pRaf1_tetramer) + Ras_pRaf1_iBRaf_tetramer + Ras_pRaf1 + Ras_pRaf1_Raf1_tetramer + (2.0 * Ras_pRaf1_tetramer) + pRaf1 + BRaf_iBRaf_dimer + Ras_Braf_iRaf1_tetramer) [tbd]
reverse rate constant
Kr
0.0 [min-1]
Expressions for MEK_dp
reaction rate
J
((Kf * pMEK) - (Kr * MEK)) [uM.min-1]
forward rate constant
Kf
kMEKdp [min-1]
global
kMEKdp
0.6 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for ERK_p
reaction rate
J
((Kf * ERK) - (Kr * pERK)) [uM.min-1]
forward rate constant
Kf
(kERKp * pMEK) [min-1]
global
kERKp
6.0E-5 [min-1.molecules-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for ERK_dp
reaction rate
J
((Kf * pERK) - (Kr * ERK)) [uM.min-1]
forward rate constant
Kf
kERKdp [min-1]
global
kERKdp
0.6 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for Ras_iBRaf_b
reaction rate
J
((Kf * iBRaf) - (Kr * Ras_iBRaf)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kiBf [molecules.um-2.min-1.uM-1]
global
B
3.6724 [tbd]
global
kiBf
2.47E-7 [molecules-1.min-1]
reverse rate constant
Kr
kiBr [min-1]
global
B
3.6724 [tbd]
global
kiBr
0.0367 [min-1]
Expressions for iBRaf_dim
reaction rate
J
((Kf * Ras_iBRaf) - (Kr * iBRaf_dimer)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1f [min-1]
global
kdR1f
0.0191 [molecules-1.min-1]
reverse rate constant
Kr
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
Expressions for iBRaf_Raf1_bind
reaction rate
J
(((Kf * Ras_Raf1) * Ras_iBRaf) - (Kr * Ras_Raf1_iBRaf_tetramer)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
reverse rate constant
Kr
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
Expressions for Raf1_iBRaf_p
reaction rate
J
((Kf * Ras_Raf1_iBRaf_tetramer) - (Kr * Ras_pRaf1_iBRaf_tetramer)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kpR1 [min-1]
global
kpR1
186.0 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for pRaf1_iBRaf_ub
reaction rate
J
((Kf * Ras_pRaf1_iBRaf_tetramer) - ((Kr * Ras_iBRaf) * Ras_pRaf1)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
reverse rate constant
Kr
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
Expressions for BRaf_dim
reaction rate
J
((Kf * Ras_BRaf) - (Kr * BRaf_dimer)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1f [min-1]
global
kdR1f
0.0191 [molecules-1.min-1]
reverse rate constant
Kr
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
Expressions for Ras_pRaf1_dp
reaction rate
J
((Kf * Ras_pRaf1) - (Kr * Ras_Raf1)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdpR1 [min-1]
global
kdpR1
0.6 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for Ras_Raf1_nfp
reaction rate
J
((Kf * Ras_Raf1) - (Kr * Ras_nfpRaf1)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
(knfpBR1 * pERK) [min-1]
global
B
3.6724 [tbd]
global
knfpBR1
6.0E-7 [min-1.molecules-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for nfpRaf1_ub
reaction rate
J
((Kf * Ras_nfpRaf1) - ((Kr * GTP_Ras) * nfpRaf1)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kfpR1r [min-1]
global
kfpR1r
2.12 [min-1]
reverse rate constant
Kr
0.0 [min-1.uM-1]
Expressions for nfpRaf1_dp
reaction rate
J
((Kf * nfpRaf1) - (Kr * Raf1)) [uM.min-1]
forward rate constant
Kf
kdpR1 [min-1]
global
kdpR1
0.6 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for BRaf_nfp
reaction rate
J
((Kf * Ras_BRaf) - (Kr * Ras_nfpBRaf)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
(knfpBR1 * pERK) [min-1]
global
B
3.6724 [tbd]
global
knfpBR1
6.0E-7 [min-1.molecules-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for nfpBRaf_ub
reaction rate
J
((Kf * Ras_nfpBRaf) - ((Kr * GTP_Ras) * nfpBRaf)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kfpBr [min-1]
global
B
3.6724 [tbd]
global
kfpBr
0.367 [min-1]
reverse rate constant
Kr
0.0 [min-1.uM-1]
Expressions for nfpBRaf_dp
reaction rate
J
((Kf * nfpBRaf) - (Kr * BRaf)) [uM.min-1]
global
B
3.6724 [tbd]
forward rate constant
Kf
kdpR1 [min-1]
global
kdpR1
0.6 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for BRaf_iBRaf_dim
reaction rate
J
(((Kf * Ras_iBRaf) * Ras_BRaf) - (Kr * BRaf_iBRaf_dimer)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
reverse rate constant
Kr
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
Expressions for Ras_iRaf_nfp
reaction rate
J
((Kf * Ras_iRaf1) - (Kr * Ras_nfpiRaf1)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
(kpR1 * pERK) [min-1]
global
kpR1
186.0 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for nfpiRaf1_ub
reaction rate
J
((Kf * Ras_nfpiRaf1) - ((Kr * nfpiRaf1) * GTP_Ras)) [molecules.um-2.min-1]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kfpR1r [min-1]
global
kfpR1r
2.12 [min-1]
reverse rate constant
Kr
0.0 [min-1.uM-1]
Expressions for nfpiRaf_dp
reaction rate
J
((Kf * nfpiRaf1) - (Kr * iRaf1)) [uM.min-1]
forward rate constant
Kf
kdpR1 [min-1]
global
kdpR1
0.6 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for Ras_iBRaf_nfp
reaction rate
J
((Kf * Ras_iBRaf) - (Kr * Ras_nfpiBRaf)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
(knfpBR1 * pERK) [min-1]
global
B
3.6724 [tbd]
global
knfpBR1
6.0E-7 [min-1.molecules-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for nfpiBRaf_ub
reaction rate
J
((Kf * Ras_nfpiBRaf) - ((Kr * nfpiBRaf) * GTP_Ras)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kfpBr [min-1]
global
B
3.6724 [tbd]
global
kfpBr
0.367 [min-1]
reverse rate constant
Kr
0.0 [min-1.uM-1]
Expressions for nfpiBRaf_dp
reaction rate
J
((Kf * nfpiBRaf) - (Kr * iBRaf)) [uM.min-1]
global
B
3.6724 [tbd]
forward rate constant
Kf
kdpR1 [min-1]
global
kdpR1
0.6 [min-1]
reverse rate constant
Kr
0.0 [min-1]
Expressions for iRaf_iBRaf_dim
reaction rate
J
(((Kf * Ras_iRaf1) * Ras_iBRaf) - (Kr * Ras_iRaf1_iBRaf1_tetramer)) [molecules.um-2.min-1]
global
B
3.6724 [tbd]
inward current density
I
0.0 [pA.um-2]
net charge valence
netValence
1.0 [1]
forward rate constant
Kf
kdR1f [um2.min-1.molecules-1]
global
kdR1f
0.0191 [molecules-1.min-1]
reverse rate constant
Kr
kdR1r [min-1]
global
kdR1r
111.0 [min-1]
Structures
pm Universal ID's
pm Text Annotations
cytoplasm Universal ID's
cytoplasm Text Annotations
Species
| Name | Structure | BioNetGen Definition | Depiction |
|---|---|---|---|
| sorafenib | cytoplasm | ||
| GTP_Ras | pm | ||
| Raf1 | cytoplasm | ||
| pRaf1 | cytoplasm | ||
| Ras_Raf1 | pm | ||
| Ras_iRaf1 | pm | ||
| Ras_pRaf1_Raf1_tetramer | pm | ||
| Ras_BRaf | pm | ||
| Ras_pRaf1 | pm | ||
| Ras_BRaf_Raf1_tetramer | pm | ||
| Ras_iRaf1_tetramer | pm | ||
| iRaf1 | cytoplasm | ||
| BRaf | cytoplasm | ||
| Ras_Braf_iRaf1_tetramer | pm | ||
| Ras_pRaf1_tetramer | pm | ||
| Ras_BRaf_pRaf1_tetramer | pm | ||
| MEK | cytoplasm | ||
| pMEK | cytoplasm | ||
| ERK | cytoplasm | ||
| iBRaf | cytoplasm | ||
| Ras_Raf1_iBRaf_tetramer | pm | ||
| Ras_pRaf1_iBRaf_tetramer | pm | ||
| pERK | cytoplasm | ||
| iBRaf_dimer | pm | ||
| BRaf_dimer | pm | ||
| Ras_iBRaf | pm | ||
| Ras_nfpRaf1 | pm | ||
| nfpRaf1 | cytoplasm | ||
| Ras_nfpBRaf | pm | ||
| nfpBRaf | cytoplasm | ||
| BRaf_iBRaf_dimer | pm | ||
| Ras_nfpiBRaf | pm | ||
| nfpiBRaf | cytoplasm | ||
| Ras_nfpiRaf1 | pm | ||
| nfpiRaf1 | cytoplasm | ||
| Ras_iRaf1_iBRaf1_tetramer | pm |
sorafenib Universal ID's
sorafenib Text Annotations
GTP_Ras Universal ID's
GTP_Ras Text Annotations
Raf1 Universal ID's
Raf1 Text Annotations
pRaf1 Universal ID's
pRaf1 Text Annotations
Ras_Raf1 Universal ID's
Ras_Raf1 Text Annotations
Ras_iRaf1 Universal ID's
Ras_iRaf1 Text Annotations
Ras_pRaf1_Raf1_tetramer Universal ID's
Ras_pRaf1_Raf1_tetramer Text Annotations
Ras_BRaf Universal ID's
Ras_BRaf Text Annotations
Ras_pRaf1 Universal ID's
Ras_pRaf1 Text Annotations
Ras_BRaf_Raf1_tetramer Universal ID's
Ras_BRaf_Raf1_tetramer Text Annotations
Ras_iRaf1_tetramer Universal ID's
Ras_iRaf1_tetramer Text Annotations
iRaf1 Universal ID's
iRaf1 Text Annotations
BRaf Universal ID's
BRaf Text Annotations
Ras_Braf_iRaf1_tetramer Universal ID's
Ras_Braf_iRaf1_tetramer Text Annotations
Ras_pRaf1_tetramer Universal ID's
Ras_pRaf1_tetramer Text Annotations
Ras_BRaf_pRaf1_tetramer Universal ID's
Ras_BRaf_pRaf1_tetramer Text Annotations
MEK Universal ID's
MEK Text Annotations
pMEK Universal ID's
pMEK Text Annotations
ERK Universal ID's
ERK Text Annotations
iBRaf Universal ID's
iBRaf Text Annotations
Ras_Raf1_iBRaf_tetramer Universal ID's
Ras_Raf1_iBRaf_tetramer Text Annotations
Ras_pRaf1_iBRaf_tetramer Universal ID's
Ras_pRaf1_iBRaf_tetramer Text Annotations
pERK Universal ID's
pERK Text Annotations
iBRaf_dimer Universal ID's
iBRaf_dimer Text Annotations
BRaf_dimer Universal ID's
BRaf_dimer Text Annotations
Ras_iBRaf Universal ID's
Ras_iBRaf Text Annotations
Ras_nfpRaf1 Universal ID's
Ras_nfpRaf1 Text Annotations
nfpRaf1 Universal ID's
nfpRaf1 Text Annotations
Ras_nfpBRaf Universal ID's
Ras_nfpBRaf Text Annotations
nfpBRaf Universal ID's
nfpBRaf Text Annotations
BRaf_iBRaf_dimer Universal ID's
BRaf_iBRaf_dimer Text Annotations
Ras_nfpiBRaf Universal ID's
Ras_nfpiBRaf Text Annotations
nfpiBRaf Universal ID's
nfpiBRaf Text Annotations
Ras_nfpiRaf1 Universal ID's
Ras_nfpiRaf1 Text Annotations
nfpiRaf1 Universal ID's
nfpiRaf1 Text Annotations
Ras_iRaf1_iBRaf1_tetramer Universal ID's
Ras_iRaf1_iBRaf1_tetramer Text Annotations
Applications
| Name | Properties | Math Type | Annotation |
|---|---|---|---|
| -sorafenib |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995 |
| +sorafenib |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | cloned from 'Raf-1 activation, +sorafenib' owned by user pmyers1995 (copied from Raf-1 activation, -sorafenib) |
| +sorafenib after 60 min EGF pretreatment |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995 |
| +sorafenib after 15 min EGF pretreatment |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from +sorafenib after 60 min EGF pretreatment) (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995 |
| +sorafenib after 30 min EGF pretreatment |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from Copy of +sorafenib after 60 min EGF pretreatment) (copied from +sorafenib after 60 min EGF pretreatment) (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995 |
| +sorafenib after 5 min EGF pretreatment |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from Copy of Copy of +sorafenib after 60 min EGF pretreatment) (copied from Copy of +sorafenib after 60 min EGF pretreatment) (copied from +sorafenib after 60 min EGF pretreatment) (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995 |
| const. active Ras-GTP, -sorafenib |
Specs -
Species Specs - Reaction Simulations |
Deterministic (ODE) Compartmental | (copied from -sorafenib) cloned from 'Raf-1 activation, -sorafenib' owned by user pmyers1995 |
-sorafenib Universal ID's
-sorafenib Text Annotations
+sorafenib Universal ID's
+sorafenib Text Annotations
+sorafenib after 60 min EGF pretreatment Universal ID's
+sorafenib after 60 min EGF pretreatment Text Annotations
+sorafenib after 15 min EGF pretreatment Universal ID's
+sorafenib after 15 min EGF pretreatment Text Annotations
+sorafenib after 30 min EGF pretreatment Universal ID's
+sorafenib after 30 min EGF pretreatment Text Annotations
+sorafenib after 5 min EGF pretreatment Universal ID's
+sorafenib after 5 min EGF pretreatment Text Annotations
const. active Ras-GTP, -sorafenib Universal ID's
const. active Ras-GTP, -sorafenib Text Annotations
Specifications (Species) - -sorafenib go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| sorafenib | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| Raf1 | 12000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| BRaf | 1000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| MEK | 500000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pMEK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| ERK | 600000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pERK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| GTP_Ras | ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Braf_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_iBRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
Specifications (Reaction) - -sorafenib go to Simulations
| Name | Enabled? |
|---|---|
| Ras_Raf1_bind | included |
| BRaf_Raf1_bind | included |
| BRaf_Raf1_phosph | included |
| Ras_pRaf1_unbind | included |
| Ras_BRaf_bind | included |
| pRaf1_Raf1_bind | included |
| pRaf1_Raf1_phosph | included |
| sorafenib_Raf1_bind_cyt | excluded |
| Ras_iRaf1_bind | excluded |
| iRaf1_iRaf1_bind | excluded |
| BRaf_iRaf1_bind | excluded |
| pRaf1_dephosph | included |
| pRaf1_pRaf1_unbind | included |
| BRaf_pRaf1_unbind | included |
| sorafenib_BRaf_bind_cyt | excluded |
| MEK_p | included |
| MEK_dp | included |
| ERK_p | included |
| ERK_dp | included |
| Ras_iBRaf_b | excluded |
| iBRaf_dim | excluded |
| iBRaf_Raf1_bind | excluded |
| Raf1_iBRaf_p | excluded |
| pRaf1_iBRaf_ub | excluded |
| BRaf_dim | included |
| Ras_pRaf1_dp | included |
| Ras_Raf1_nfp | included |
| nfpRaf1_ub | included |
| nfpRaf1_dp | included |
| BRaf_nfp | included |
| nfpBRaf_ub | included |
| nfpBRaf_dp | included |
| BRaf_iBRaf_dim | excluded |
| Ras_iRaf_nfp | excluded |
| nfpiRaf1_ub | excluded |
| nfpiRaf_dp | excluded |
| Ras_iBRaf_nfp | excluded |
| nfpiBRaf_ub | excluded |
| nfpiBRaf_dp | excluded |
| iRaf_iBRaf_dim | excluded |
Simulations - -sorafenib go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| 60 min | 60.0 |
KeepEvery 1 KeepAtMost 1000 |
| Fitted binding rates | 60.0 |
KeepEvery 1 KeepAtMost 1000 |
-sorafenib Universal ID's
-sorafenib Text Annotations
-sorafenib Universal ID's
-sorafenib Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial1069339151
(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 | pm |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - +sorafenib go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| sorafenib | 10.0 [uM] | 0.0 [um2/min] | cytoplasm |
| Raf1 | 12000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| BRaf | 1000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| MEK | 500000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pMEK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| ERK | 600000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pERK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| GTP_Ras | ((As * t * exp(( - t / Bs))) + (Cs * t / (t + Ds))) [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Braf_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_iBRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
Specifications (Reaction) - +sorafenib go to Simulations
| Name | Enabled? |
|---|---|
| Ras_Raf1_bind | included |
| BRaf_Raf1_bind | included |
| BRaf_Raf1_phosph | included |
| Ras_pRaf1_unbind | included |
| Ras_BRaf_bind | included |
| pRaf1_Raf1_bind | included |
| pRaf1_Raf1_phosph | included |
| sorafenib_Raf1_bind_cyt | included |
| Ras_iRaf1_bind | included |
| iRaf1_iRaf1_bind | included |
| BRaf_iRaf1_bind | included |
| pRaf1_dephosph | included |
| pRaf1_pRaf1_unbind | included |
| BRaf_pRaf1_unbind | included |
| sorafenib_BRaf_bind_cyt | included |
| MEK_p | included |
| MEK_dp | included |
| ERK_p | included |
| ERK_dp | included |
| Ras_iBRaf_b | included |
| iBRaf_dim | included |
| iBRaf_Raf1_bind | included |
| Raf1_iBRaf_p | included |
| pRaf1_iBRaf_ub | included |
| BRaf_dim | included |
| Ras_pRaf1_dp | included |
| Ras_Raf1_nfp | included |
| nfpRaf1_ub | included |
| nfpRaf1_dp | included |
| BRaf_nfp | included |
| nfpBRaf_ub | included |
| nfpBRaf_dp | included |
| BRaf_iBRaf_dim | included |
| Ras_iRaf_nfp | included |
| nfpiRaf1_ub | included |
| nfpiRaf_dp | included |
| Ras_iBRaf_nfp | included |
| nfpiBRaf_ub | included |
| nfpiBRaf_dp | included |
| iRaf_iBRaf_dim | included |
Simulations - +sorafenib go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Fitted binding | 60.0 |
KeepEvery 1 KeepAtMost 1000 |
+sorafenib Universal ID's
+sorafenib Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial1102832951
(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 | pm |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - +sorafenib after 60 min EGF pretreatment go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| sorafenib | (10.0 * (t > 60.0)) [uM] | 0.0 [um2/min] | cytoplasm |
| Raf1 | 12000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| BRaf | 1000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| MEK | 500000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pMEK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| ERK | 600000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pERK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| GTP_Ras | ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Braf_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_iBRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
Specifications (Reaction) - +sorafenib after 60 min EGF pretreatment go to Simulations
| Name | Enabled? |
|---|---|
| Ras_Raf1_bind | included |
| BRaf_Raf1_bind | included |
| BRaf_Raf1_phosph | included |
| Ras_pRaf1_unbind | included |
| Ras_BRaf_bind | included |
| pRaf1_Raf1_bind | included |
| pRaf1_Raf1_phosph | included |
| sorafenib_Raf1_bind_cyt | included |
| Ras_iRaf1_bind | included |
| iRaf1_iRaf1_bind | included |
| BRaf_iRaf1_bind | included |
| pRaf1_dephosph | included |
| pRaf1_pRaf1_unbind | included |
| BRaf_pRaf1_unbind | included |
| sorafenib_BRaf_bind_cyt | included |
| MEK_p | included |
| MEK_dp | included |
| ERK_p | included |
| ERK_dp | included |
| Ras_iBRaf_b | included |
| iBRaf_dim | included |
| iBRaf_Raf1_bind | included |
| Raf1_iBRaf_p | included |
| pRaf1_iBRaf_ub | included |
| BRaf_dim | included |
| Ras_pRaf1_dp | included |
| Ras_Raf1_nfp | included |
| nfpRaf1_ub | included |
| nfpRaf1_dp | included |
| BRaf_nfp | included |
| nfpBRaf_ub | included |
| nfpBRaf_dp | included |
| BRaf_iBRaf_dim | included |
| Ras_iRaf_nfp | included |
| nfpiRaf1_ub | included |
| nfpiRaf_dp | included |
| Ras_iBRaf_nfp | included |
| nfpiBRaf_ub | included |
| nfpiBRaf_dp | included |
| iRaf_iBRaf_dim | included |
Simulations - +sorafenib after 60 min EGF pretreatment go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| 60 min EGF pretreat | 80.0 |
KeepEvery 1 KeepAtMost 1000 |
+sorafenib after 60 min EGF pretreatment Universal ID's
+sorafenib after 60 min EGF pretreatment Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial1069339151
(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 | pm |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - +sorafenib after 15 min EGF pretreatment go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| sorafenib | (10.0 * (t > 15.0)) [uM] | 0.0 [um2/min] | cytoplasm |
| Raf1 | 12000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| BRaf | 1000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| MEK | 500000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pMEK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| ERK | 600000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pERK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| GTP_Ras | ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Braf_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_iBRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
Specifications (Reaction) - +sorafenib after 15 min EGF pretreatment go to Simulations
| Name | Enabled? |
|---|---|
| Ras_Raf1_bind | included |
| BRaf_Raf1_bind | included |
| BRaf_Raf1_phosph | included |
| Ras_pRaf1_unbind | included |
| Ras_BRaf_bind | included |
| pRaf1_Raf1_bind | included |
| pRaf1_Raf1_phosph | included |
| sorafenib_Raf1_bind_cyt | included |
| Ras_iRaf1_bind | included |
| iRaf1_iRaf1_bind | included |
| BRaf_iRaf1_bind | included |
| pRaf1_dephosph | included |
| pRaf1_pRaf1_unbind | included |
| BRaf_pRaf1_unbind | included |
| sorafenib_BRaf_bind_cyt | included |
| MEK_p | included |
| MEK_dp | included |
| ERK_p | included |
| ERK_dp | included |
| Ras_iBRaf_b | included |
| iBRaf_dim | included |
| iBRaf_Raf1_bind | included |
| Raf1_iBRaf_p | included |
| pRaf1_iBRaf_ub | included |
| BRaf_dim | included |
| Ras_pRaf1_dp | included |
| Ras_Raf1_nfp | included |
| nfpRaf1_ub | included |
| nfpRaf1_dp | included |
| BRaf_nfp | included |
| nfpBRaf_ub | included |
| nfpBRaf_dp | included |
| BRaf_iBRaf_dim | included |
| Ras_iRaf_nfp | included |
| nfpiRaf1_ub | included |
| nfpiRaf_dp | included |
| Ras_iBRaf_nfp | included |
| nfpiBRaf_ub | included |
| nfpiBRaf_dp | included |
| iRaf_iBRaf_dim | included |
Simulations - +sorafenib after 15 min EGF pretreatment go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| 15 min EGF pretreat | 35.0 |
KeepEvery 1 KeepAtMost 1000 |
+sorafenib after 15 min EGF pretreatment Universal ID's
+sorafenib after 15 min EGF pretreatment Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial1069339151
(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 | pm |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - +sorafenib after 30 min EGF pretreatment go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| sorafenib | (10.0 * (t > 30.0)) [uM] | 0.0 [um2/min] | cytoplasm |
| Raf1 | 12000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| BRaf | 1000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| MEK | 500000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pMEK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| ERK | 600000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pERK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| GTP_Ras | ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Braf_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_iBRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
Specifications (Reaction) - +sorafenib after 30 min EGF pretreatment go to Simulations
| Name | Enabled? |
|---|---|
| Ras_Raf1_bind | included |
| BRaf_Raf1_bind | included |
| BRaf_Raf1_phosph | included |
| Ras_pRaf1_unbind | included |
| Ras_BRaf_bind | included |
| pRaf1_Raf1_bind | included |
| pRaf1_Raf1_phosph | included |
| sorafenib_Raf1_bind_cyt | included |
| Ras_iRaf1_bind | included |
| iRaf1_iRaf1_bind | included |
| BRaf_iRaf1_bind | included |
| pRaf1_dephosph | included |
| pRaf1_pRaf1_unbind | included |
| BRaf_pRaf1_unbind | included |
| sorafenib_BRaf_bind_cyt | included |
| MEK_p | included |
| MEK_dp | included |
| ERK_p | included |
| ERK_dp | included |
| Ras_iBRaf_b | included |
| iBRaf_dim | included |
| iBRaf_Raf1_bind | included |
| Raf1_iBRaf_p | included |
| pRaf1_iBRaf_ub | included |
| BRaf_dim | included |
| Ras_pRaf1_dp | included |
| Ras_Raf1_nfp | included |
| nfpRaf1_ub | included |
| nfpRaf1_dp | included |
| BRaf_nfp | included |
| nfpBRaf_ub | included |
| nfpBRaf_dp | included |
| BRaf_iBRaf_dim | included |
| Ras_iRaf_nfp | included |
| nfpiRaf1_ub | included |
| nfpiRaf_dp | included |
| Ras_iBRaf_nfp | included |
| nfpiBRaf_ub | included |
| nfpiBRaf_dp | included |
| iRaf_iBRaf_dim | included |
Simulations - +sorafenib after 30 min EGF pretreatment go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| 30 min EGF pretreat | 50.0 |
KeepEvery 1 KeepAtMost 1000 |
+sorafenib after 30 min EGF pretreatment Universal ID's
+sorafenib after 30 min EGF pretreatment Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial1069339151
(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 | pm |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - +sorafenib after 5 min EGF pretreatment go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| sorafenib | (10.0 * (t > 5.0)) [uM] | 0.0 [um2/min] | cytoplasm |
| Raf1 | 12000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| BRaf | 1000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| MEK | 500000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pMEK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| ERK | 600000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pERK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| GTP_Ras | ((A * t * exp(( - t / B))) + (C * t / (t + D))) [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Braf_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_iBRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
Specifications (Reaction) - +sorafenib after 5 min EGF pretreatment go to Simulations
| Name | Enabled? |
|---|---|
| Ras_Raf1_bind | included |
| BRaf_Raf1_bind | included |
| BRaf_Raf1_phosph | included |
| Ras_pRaf1_unbind | included |
| Ras_BRaf_bind | included |
| pRaf1_Raf1_bind | included |
| pRaf1_Raf1_phosph | included |
| sorafenib_Raf1_bind_cyt | included |
| Ras_iRaf1_bind | included |
| iRaf1_iRaf1_bind | included |
| BRaf_iRaf1_bind | included |
| pRaf1_dephosph | included |
| pRaf1_pRaf1_unbind | included |
| BRaf_pRaf1_unbind | included |
| sorafenib_BRaf_bind_cyt | included |
| MEK_p | included |
| MEK_dp | included |
| ERK_p | included |
| ERK_dp | included |
| Ras_iBRaf_b | included |
| iBRaf_dim | included |
| iBRaf_Raf1_bind | included |
| Raf1_iBRaf_p | included |
| pRaf1_iBRaf_ub | included |
| BRaf_dim | included |
| Ras_pRaf1_dp | included |
| Ras_Raf1_nfp | included |
| nfpRaf1_ub | included |
| nfpRaf1_dp | included |
| BRaf_nfp | included |
| nfpBRaf_ub | included |
| nfpBRaf_dp | included |
| BRaf_iBRaf_dim | included |
| Ras_iRaf_nfp | included |
| nfpiRaf1_ub | included |
| nfpiRaf_dp | included |
| Ras_iBRaf_nfp | included |
| nfpiBRaf_ub | included |
| nfpiBRaf_dp | included |
| iRaf_iBRaf_dim | included |
Simulations - +sorafenib after 5 min EGF pretreatment go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| 5 min EGF pretreat | 25.0 |
KeepEvery 1 KeepAtMost 1000 |
+sorafenib after 5 min EGF pretreatment Universal ID's
+sorafenib after 5 min EGF pretreatment Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial1069339151
(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 | pm |
Events
| Name | Variable | Rate Expression |
|---|
Specifications (Species) - const. active Ras-GTP, -sorafenib go to Simulations
| Species | Initial Condition | Diffusion Constant | Structure |
|---|---|---|---|
| sorafenib | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| Raf1 | 12000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| BRaf | 1000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| MEK | 500000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pMEK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| ERK | 600000.0 [uM] | 0.0 [um2/min] | cytoplasm |
| iBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| pERK | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | cytoplasm |
| GTP_Ras | 27000.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_Raf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Braf_iRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_BRaf_pRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_Raf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_pRaf1_iBRaf_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
| iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| BRaf_iBRaf_dimer | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiBRaf | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_nfpiRaf1 | 0.0 [uM] | 0.0 [um2/min] | pm |
| Ras_iRaf1_iBRaf1_tetramer | 0.0 [uM] | 0.0 [um2/min] | pm |
Specifications (Reaction) - const. active Ras-GTP, -sorafenib go to Simulations
| Name | Enabled? |
|---|---|
| Ras_Raf1_bind | included |
| BRaf_Raf1_bind | included |
| BRaf_Raf1_phosph | included |
| Ras_pRaf1_unbind | included |
| Ras_BRaf_bind | included |
| pRaf1_Raf1_bind | included |
| pRaf1_Raf1_phosph | included |
| sorafenib_Raf1_bind_cyt | excluded |
| Ras_iRaf1_bind | excluded |
| iRaf1_iRaf1_bind | excluded |
| BRaf_iRaf1_bind | excluded |
| pRaf1_dephosph | included |
| pRaf1_pRaf1_unbind | included |
| BRaf_pRaf1_unbind | included |
| sorafenib_BRaf_bind_cyt | included |
| MEK_p | included |
| MEK_dp | included |
| ERK_p | included |
| ERK_dp | included |
| Ras_iBRaf_b | excluded |
| iBRaf_dim | excluded |
| iBRaf_Raf1_bind | excluded |
| Raf1_iBRaf_p | excluded |
| pRaf1_iBRaf_ub | excluded |
| BRaf_dim | included |
| Ras_pRaf1_dp | included |
| Ras_Raf1_nfp | included |
| nfpRaf1_ub | included |
| nfpRaf1_dp | included |
| BRaf_nfp | included |
| nfpBRaf_ub | included |
| nfpBRaf_dp | included |
| BRaf_iBRaf_dim | excluded |
| Ras_iRaf_nfp | excluded |
| nfpiRaf1_ub | excluded |
| nfpiRaf_dp | excluded |
| Ras_iBRaf_nfp | excluded |
| nfpiBRaf_ub | excluded |
| nfpiBRaf_dp | excluded |
| iRaf_iBRaf_dim | excluded |
Simulations - const. active Ras-GTP, -sorafenib go to Specifications
| Name | End Time | Output Options |
|---|---|---|
| Simulation0 | 60.0 |
KeepEvery 1 KeepAtMost 1000 |
| 10x Ras | 60.0 |
KeepEvery 1 KeepAtMost 1000 |
const. active Ras-GTP, -sorafenib Universal ID's
const. active Ras-GTP, -sorafenib Text Annotations
const. active Ras-GTP, -sorafenib Universal ID's
const. active Ras-GTP, -sorafenib Text Annotations
Assignments
| Name | Variable | Assignment Function Expression |
|---|
Events
| Name | Trigger Type | Variable Assignment |
|---|
Geometry non-spatial757173534
(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 | pm |
Events
| Name | Variable | Rate Expression |
|---|
Global Parameters
| Name | Expression |
|---|---|
| kSon | 100000.0 [uM-1.min-1] |
| kSoff | 420.0 [min-1] |
| kpR1 | 186.0 [min-1] |
| kdR1f | 0.0191 [molecules-1.min-1] |
| kR1f | 1.84E-7 [molecules.min-1] |
| kR1r | 0.212 [min-1] |
| kBf | 2.47E-7 [min-1.molecules-1] |
| kBr | 0.0367 [min-1] |
| kdR1r | 111.0 [min-1] |
| kdpR1 | 0.6 [min-1] |
| boundRaf_frac_parameter | (Raf1_pm_param / (Raf1_cyt_param + Raf1_pm_param))[tbd] |
| A | 20671.0 [tbd] |
| B | 3.6724 [tbd] |
| C | 6.7089E16 [tbd] |
| RasGTP_parameter | (GTP_Ras + (2.0 * (Ras_iRaf1_tetramer + Ras_Braf_iRaf1_tetramer + Ras_BRaf_Raf1_tetramer + Ras_pRaf1_Raf1_tetramer + Ras_BRaf_pRaf1_tetramer + Ras_pRaf1_tetramer + BRaf_dimer + BRaf_iBRaf_dimer + iBRaf_dimer + Ras_iRaf1_iBRaf1_tetramer + Ras_Raf1_iBRaf_tetramer + Ras_pRaf1_iBRaf_tetramer)) + Ras_BRaf + Ras_iRaf1 + Ras_pRaf1 + Ras_Raf1 + Ras_nfpRaf1 + Ras_nfpiRaf1 + Ras_iBRaf + Ras_nfpiBRaf + Ras_nfpBRaf)[tbd] |
| kiR1f | 1.84E-7 [min-1.molecules-1] |
| kiR1r | 0.212 [min-1] |
| Raf1_pm_param | (Ras_pRaf1 + (2.0 * Ras_pRaf1_Raf1_tetramer) + Ras_BRaf_Raf1_tetramer + Ras_iRaf1 + Ras_Raf1 + (2.0 * Ras_iRaf1_tetramer) + Ras_Braf_iRaf1_tetramer + Ras_BRaf_pRaf1_tetramer + (2.0 * Ras_pRaf1_tetramer) + Ras_nfpiRaf1 + Ras_nfpRaf1 + Ras_iRaf1_iBRaf1_tetramer + Ras_Raf1_iBRaf_tetramer + Ras_pRaf1_iBRaf_tetramer)[tbd] |
| Raf1_cyt_param | (Raf1 + pRaf1 + iRaf1 + nfpRaf1 + nfpiRaf1)[tbd] |
| kMEKp | 6.0E-6[molecules-1.min-1] |
| active_Raf | ((2.0 * BRaf_dimer) + Ras_BRaf_Raf1_tetramer + (2.0 * Ras_BRaf_pRaf1_tetramer) + Ras_pRaf1_iBRaf_tetramer + Ras_pRaf1 + Ras_pRaf1_Raf1_tetramer + (2.0 * Ras_pRaf1_tetramer) + pRaf1 + BRaf_iBRaf_dimer + Ras_Braf_iRaf1_tetramer)[tbd] |
| kERKp | 6.0E-5[min-1.molecules-1] |
| kERKdp | 0.6[min-1] |
| kMEKdp | 0.6[min-1] |
| kiBf | 2.47E-7[molecules-1.min-1] |
| kiBr | 0.0367[min-1] |
| kfpR1r | 2.12[min-1] |
| kfpBr | 0.367[min-1] |
| knfpBR1 | 6.0E-7[min-1.molecules-1] |
| D | 1.1735E15[tbd] |
| As | 21930.665775907[tbd] |
| Bs | 3.30082007598438[tbd] |
| Cs | 5.37755813880742E16[tbd] |
| Ds | 1.42262832362309E15[tbd] |