| |
Name /
Accession
No. | Accession Type /
Entry Date | Accession statistics | CamKII statistics | Species /
Tissue | Cell Compartment /
Source | Methodology /
Model_
Implementation |
| 1 | AMPAR_CaMKII_
strong_coupling
Accession No. : 64 | Network /
2005-07-19 00:00:00 | Molecule = 133
Enzyme = 158
Reaction = 57
| Molecule = 21
Enzyme = 23
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | This is a model of tight coupling between the AMPAR trafficking bistability, and the CaMKII autophosphorylation bistability. In this model, the CaMKII activity is self sustaining only when AMPAR is turned on. Further, CaMKII turns on when AMPAR is turned on. |
| | |
| 2 | AMPAR_CaMKII_
weak_coupling
Accession No. : 65 | Network /
2005-07-21 00:00:00 | Molecule = 134
Enzyme = 158
Reaction = 57
| Molecule = 22
Enzyme = 28
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | This is a model of weak coupling between the AMPAR traffikcing bistability, and the CaMKII autophosphorylation bistability. In this model, there are three stable states: Both off, AMPAR on, or both on. The fourth possible state: CaMKII on but AMPAR off, is not truly stable, since over the course of hours the AMPAR also turns on. |
| | |
| 3 | 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 |
|
| 4 | CaMKIII
Accession No. : 90 | Network /
2009-02-12 00:00:00 | Molecule = 19
Enzyme = 5
Reaction = 7
| Molecule = 4
Enzyme = 4
Reaction = 2
| General Mammalian /
Brain | Surface, Cytosol, Nucleus /
Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation,Approximate implementation |
| | CaMKIII is activated by Ca2+ and inactivated by S6K. Since CaMKIII inhibits eEF2, the net effect of Ca2+ on elongation is inhibitory and of S6K is excitatory |
| | | Format | File | | Native Format (GENESIS format) | acc90.g |
|
| 5 | 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. |
| | |
| 6 | CaMKII_model3
Accession No. : 63 | Network /
2005-07-19 00:00:00 | Molecule = 76
Enzyme = 40
Reaction = 39
| Molecule = 21
Enzyme = 7
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | This is the complete model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 includes PKA regulatory input. This has little effect on the deterministic calculations, but the PKA pathway introduces a lot of noise which causes a difference in stochastic runs. |
| | |
| 7 | CaMKII_noPKA_
model3
Accession No. : 62 | Network /
2005-07-19 00:00:00 | Molecule = 53
Enzyme = 32
Reaction = 26
| Molecule = 21
Enzyme = 7
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | This is the model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 does not include the full PKA regulatory pathway, and instead has a predefined initial amount of active PKA. |
| | |
| 8 | 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 |
|
| 9 | syn_CaMKIII
Accession No. : 114 | Pathway /
2022-10-01 00:12:23 | Molecule = 8
Enzyme = 0
Reaction = 3
| Molecule = 2
Enzyme = 0
Reaction = 0
| Rodent /
Brain | Synapse /
Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621. | Quantitative fit to experiments /
HillTau implementation |
| | This model was used to generate Fig 3 supp A to F in Bhalla US. HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks. PLoS Comput Biol 2021 Nov 29;17(11):e1009621. |
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indicates that ordering is done according to ascending or descending order.
or Pathway 