| |
Name /
Accession
No. | Accession Type /
Entry Date | Accession statistics | CamKII statistics | Species /
Tissue | Cell Compartment /
Source | Methodology /
Model_
Implementation |
| 1 | fig3_CaMKII
Accession No. : 2 | Network /
2001-11-07 00:00:00 | Molecule = 59
Enzyme = 29
Reaction = 29
| Molecule = 9
Enzyme = 4
Reaction = 1
| Generic mammalian /
Neuronal | Synapse /
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | This is the model file for figure 3 from Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. It is a model of the Ca activation of CaMKII and other CaM-activated enzymes. It includes the regulatory phosphatases PP1 and PP2B (Calcineurin) acting on CaMKII and also includes CaM-activated adenylyl cyclase and PKA in the synapse.
Demonstration script files for generating the figures in the paper, including figure 3, are available here. |
| | | Format | File | | Native Format (GENESIS format) | acc2.g | | GENESIS Format (Annotated version) | Anno_acc2.g |
|
| 2 | fig4_synapse
Accession No. : 3 | Network /
2001-11-07 00:00:00 | Molecule = 122
Enzyme = 56
Reaction = 70
| Molecule = 9
Enzyme = 4
Reaction = 1
| Generic mammalian /
Neuronal | Synapse /
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) | Quantitative match to experiments, Qualitative, Hypothetical /
Exact GENESIS implementation |
| | This is the composite model of 4 kinases: PKC, MAPK, PKA and CaMKII and numerous regulatory pathways involved in synaptic signaling. From Bhalla US and Iyengar R. Science (1999) 283(5400):381-7.This model comes from figure 4 of that paper.
Demonstration script files for generating the figures in the paper, including figure 4, are available here. |
| | | Format | File | | Native Format (GENESIS format) | acc3.g | | GENESIS Format (Annotated version) | Anno_acc3.g |
|
| 3 | Synaptic_
Network
Accession No. : 16 | Network /
2001-12-12 00:00:00 | Molecule = 148
Enzyme = 63
Reaction = 84
| Molecule = 8
Enzyme = 4
Reaction = 1
| Generic mammalian /
Neuronal | Synapse /
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | This model is an annotated version of the synaptic signaling network.
The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated.
Bhalla US Biophys J. 2002 Aug;83(2):740-52
Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62 |
| | | Format | File | | Native Format (GENESIS format) | acc16.g | | GENESIS Format (Annotated version) | Anno_acc16.g |
|
| 4 | NOS_Phosph_
regulation
Accession No. : 20 | Pathway /
2001-12-25 00:00:00 | Molecule = 10
Enzyme = 4
Reaction = 2
| Molecule = 1
Enzyme = 1
Reaction = 0
| rat; Mammalian /
Brain - Neuronal; expressed in E.coli | Cytosol /
In-house | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | This model features the phosphorylation of rat brain neuronal NOS expressed in E. coli or Sf9 cells, which leads to a decrease in Vmax of the phosphorylated enzyme, with little change of both the Km for L-arginine and Kact for CaM. This is based on Hayashi Y. et al. J Biol Chem. (1999) 274(29):20597-602. They report of phosphorylatin being carried out by CaM kinases I alpha, II alpha and IV. The rates used have been obtained from their paper and from other reported experimental data. |
| | |
| 5 | NonOsc_Ca_
IP3metabolism
Accession No. : 23 | Network /
2002-01-07 00:00:00 | Molecule = 134
Enzyme = 48
Reaction = 81
| Molecule = 8
Enzyme = 8
Reaction = 1
| Generic mammalian /
Brain - Neuronal | Cytosol /
Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Approximate implementation |
| | This network models detailed metabolism of Ins(145)P3, integrated with GPCR mediated PLCbeta activation and Ca release by the InsP3 receptor in the neuron. The calcium response is non-oscillatory. Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. |
| | | Format | File | | Native Format (GENESIS format) | acc23.g | | GENESIS Format (Annotated version) | Anno_acc23.g |
|
| 6 | Osc_Ca_
IP3metabolism
Accession No. : 24 | Network /
2002-01-08 00:00:00 | Molecule = 137
Enzyme = 49
Reaction = 82
| Molecule = 8
Enzyme = 8
Reaction = 1
| Generic mammalian /
Brain - Neuronal | Cytosol /
Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Approximate implementation |
| | This network models an oscillatory calcium response to GPCR mediated PLCbeta activation, alongwith detailed InsP3 metabolism in the neuron. It differs from the NonOsc_Ca_IP3metabolism network in the CaRegulation module and in InsP3 receptor kinetics. Details of InsP3 receptor kinetics have been adapted from the Othmer-Tang model for oscillatory Ca dynamics. Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. |
| | | Format | File | | Native Format (GENESIS format) | acc24.g | | GENESIS Format (Annotated version) | Anno_acc24.g |
|
| 7 | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | Network /
2002-04-03 00:00:00 | Molecule = 135
Enzyme = 42
Reaction = 90
| Molecule = 8
Enzyme = 8
Reaction = 1
| Generic mammalian /
Brain - Neuronal | Cytosol /
Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | This network models detailed metabolism of Ins(145)P3, integrated with GPCR mediated PLCbeta activation and Ca release by the InsP3 receptor in the neuron. It is similar to the NonOsc_Ca_IP3metab model (accession 23) except that some enzymes have been modified to have reversible kinetics rather than Michaelis-Menten kinetics. These modified enzymes belong to the groups: IP4-system, IP3-3K, 145_dephos and 134_dephos. Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. |
| | | Format | File | | Native Format (GENESIS format) | acc31.g | | GENESIS Format (Annotated version) | Anno_acc31.g |
|
| 8 | Osc_Ca_
IP3metabolism
Accession No. : 32 | Network /
2002-04-03 00:00:00 | Molecule = 138
Enzyme = 43
Reaction = 91
| Molecule = 8
Enzyme = 8
Reaction = 1
| Generic mammalian /
Brain - Neuronal | Cytosol /
Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | This network models an oscillatory calcium response to GPCR mediated PLCbeta activation, alongwith detailed InsP3 metabolism in the neuron. It is similar to the Osc_Ca_IP3metab model (accession 24) except that some enzymes in the InsP3 metabolism network have been modified to have reversible kinetics rather than Michaelis-Menten kinetics. The modified enzymes belong to the groups: IP4-system, IP3-3K, 145_dephos and 134_dephos. Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. |
| | | Format | File | | Native Format (GENESIS format) | acc32.g | | GENESIS Format (Annotated version) | Anno_acc32.g |
|
| 9 | CaMKII
Accession No. : 33 | Network /
2002-08-21 00:00:00 | Molecule = 23
Enzyme = 2
Reaction = 27
| Molecule = 8
Enzyme = 2
Reaction = 9
| Generic mammalian /
Brain - Neuronal | Synapse /
William R. Holmes J Comput Neurosci. (2000) 8(1):65-85 ( peer-reviewed publication ) | Qualitative /
Approximate implementation |
| | This is a deterministic, point kinetics approximation to the dendritic spine CaMKII model described in William R. Holmes J Comput Neurosci. (2000) 8(1):65-85. Rates are the same but the responses differ somewhat because this model does not include the stochastic and diffusive calculations of the original. |
| | | Format | File | | Native Format (GENESIS format) | acc33.g | | GENESIS Format (Annotated version) | Anno_acc33.g |
|
| 10 | CaMKII_2003
Accession No. : 49 | Network /
2003-04-28 00:00:00 | Molecule = 31
Enzyme = 18
Reaction = 15
| Molecule = 7
Enzyme = 4
Reaction = 1
| Generic mammalian /
Brain - Neuronal | Synapse /
Bhalla US. Biophys J. 2004 Aug;87(2):733-44. ( peer-reviewed publication ). | Qualitative /
Exact GENESIS implementation |
| | Model of regulation of CaMKII by Calcium, including parallel excitatory input from CaM and inhibitory input from PP1 as regulated by Calcineurin and PKA. Cell type: neuronal.
Bhalla US. Biophys J. 2004 Aug;87(2):733-44. |
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indicates that ordering is done according to ascending or descending order.
or Pathway 