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From Yeast Pheromone Model

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All pages
All pages
AboutAdditional resources
Alpha factor
Assumptions to re-test with full modelAssumptions to vet with othersAvogadros number
BNG
BioNetGen
Brief overview of the model
Brief overview of the organization of the modelCellCell cycle regulation of pheromone response
Cell tot concCell volumeCode for Thomson, Benjamin et al.
Contributing to the Site
Contributing to the site
Conventions
CopyrightDeleteMoleculesDig1
Dig1/Dig2/Ste12/MAPK binding rate constant constraintsDig1/Dig2/Ste12/Tec1 interactions
Dig1/Dig2/Ste12 binding
Dig1/Dig2/Ste12 phosphorylationDig1 numDig1 tot conc
Dig2Dig2 numDig2 tot conc
EtiquetteExtracted model logExtracting the model
FAQ
FAR1
Far1
Far1/Fus3/Kss1 interactions
Far1/MAPK interactionsFar1 num
Far1 tot concFus3Fus3/Gpa1/Ste4 interactions
Fus3 Kss1 Kd preference factorFus3 Kss1 preference PO4 factorFus3 num
Fus3 target phosphorylation properties
Fus3 tot conc
GPA1
GTP modulating factor
G Protein
G protein
G protein nucleotide hydrolysis/exchange
G proteins
Galpha(Gpa1) synthesis/degradation
Gbeta(Ste4)/Ggamma(Ste18) interaction
Getting Started
Getting started
Gpa1Gpa1 numGpa1 synthesis/degradation
Gpa1 tot conc
How to Join
How to join
Instances of modelsIssues to address
KSS1
Kcat Fus3pT Dig1 PO4Kcat Fus3pT Dig2 PO4Kcat Fus3pT Far1 PO4
Kcat Fus3pTpY Dig1 PO4Kcat Fus3pTpY Dig2 PO4Kcat Fus3pTpY Far1 PO4
Kcat Fus3pY Dig1 PO4Kcat Fus3pY Dig2 PO4Kcat Fus3pY Far1 PO4
Kcat Gpa1GDP GTPKcat Gpa1GTP GDPKcat Kss1pT Dig1 PO4
Kcat Kss1pT Dig2 PO4Kcat Kss1pT Far1 PO4Kcat Kss1pTpY Dig1 PO4
Kcat Kss1pTpY Dig2 PO4Kcat Kss1pTpY Far1 PO4Kcat Kss1pY Dig1 PO4
Kcat Kss1pY Dig2 PO4Kcat Kss1pY Far1 PO4Kcat MAPKpT Sst2 PO4
Kcat MAPKpT Ste11 PO4Kcat MAPKpTpY Sst2 PO4Kcat MAPKpTpY Ste11 PO4
Kcat MAPKpY Sst2 PO4Kcat MAPKpY Ste11 PO4Kcat Msg5 MAPK PO4
Kcat PheromoneSte2Gpa1GDP GTPKcat Ptp MAPK PO4Kcat Sst2Gpa1GTP GDP
Kcat Ste11pSSte5Ste5Ste7 pSKcat Ste11pSSte5Ste5Ste7pS pTKcat Ste11pSpSSte5Ste5Ste7 pS
Kcat Ste11pSpSSte5Ste5Ste7pS pTKcat Ste11pSpSpTSte5Ste5Ste7 pSKcat Ste11pSpSpTSte5Ste5Ste7pS pT
Kcat Ste20Ste4Ste18Ste5Ste11 pSKcat Ste20Ste4Ste18Ste5Ste11pS pSKcat Ste20Ste4Ste18Ste5Ste11pSpS pT
Kcat Ste5Ste7pSFus3 pTKcat Ste5Ste7pSFus3 pYKcat Ste5Ste7pSFus3pT pY
Kcat Ste5Ste7pSFus3pY pTKcat Ste5Ste7pSpTFus3 pTKcat Ste5Ste7pSpTFus3 pY
Kcat Ste5Ste7pSpTFus3pT pYKcat Ste5Ste7pSpTFus3pY pTKcat Ste7pSKss1 pT
Kcat Ste7pSKss1 pYKcat Ste7pSKss1pT pYKcat Ste7pSKss1pY pT
Kcat Ste7pSpTKss1 pTKcat Ste7pSpTKss1 pYKcat Ste7pSpTKss1pT pY
Kcat Ste7pSpTKss1pY pTKcat YckPheromoneSte2 PO4Kcat YckSte2 PO4
Kcat nonspecific dephosphKd Fus3pTpY Dig1Kd Fus3pTpY Dig2
Kd Fus3pTpY Far1Kd Kss1pTpY Dig1Kd Kss1pTpY Dig2
Kd Kss1pTpY Far1Kd Msg5 MAPKKd Pheromone Ste2
Kd Ste5 Fus3Kd Ste5 Kss1Kd Ste5 Ste11
Kd Ste5 Ste7Kd Ste7 MAPKKdeg Fus3pT Ste12
Kdeg Fus3pT Ste7Kdeg Fus3pTpY Ste12Kdeg Fus3pTpY Ste7
Kdeg Fus3pY Ste12Kdeg Fus3pY Ste7Kdeg Gpa1
Kdeg Kss1pT Ste12Kdeg Kss1pT Ste7Kdeg Kss1pTpY Ste12
Kdeg Kss1pTpY Ste7Kdeg Kss1pY Ste12Kdeg Kss1pY Ste7
Kdeg Sst2Kdeg Sst2 PO4Kdeg Ste11
Kdeg Ste11 PO4Kdeg Ste2 PO4Kdilution
Kdilutionsynth Dig1Kdilutionsynth Dig2Kdilutionsynth Far1
Kdilutionsynth Fus3Kdilutionsynth Gpa1Kdilutionsynth Kss1
Kdilutionsynth Msg5Kdilutionsynth PtpKdilutionsynth Sst2
Kdilutionsynth Ste11Kdilutionsynth Ste12Kdilutionsynth Ste2
Kdilutionsynth Ste20Kdilutionsynth Ste4Ste18Kdilutionsynth Ste5
Kdilutionsynth Ste7Kdilutionsynth YckKdilutionsynth pheromone
Kinternalization Ste2Km deg Fus3pT Ste12Km deg Fus3pT Ste7
Km deg Fus3pTpY Ste12Km deg Fus3pTpY Ste7Km deg Fus3pY Ste12
Km deg Fus3pY Ste7Km deg Kss1pT Ste12Km deg Kss1pT Ste7
Km deg Kss1pTpY Ste12Km deg Kss1pTpY Ste7Km deg Kss1pY Ste12
Km deg Kss1pY Ste7Km synth Ste12 Dig2Km synth Ste12 Far1
Km synth Ste12 Fus3Km synth Ste12 Gpa1Km synth Ste12 Msg5
Km synth Ste12 PtpKm synth Ste12 Sst2Km synth Ste12 Ste12
Km synth Ste12 Ste2Koff Fus3pT Dig1Koff Fus3pT Dig2
Koff Fus3pT Far1Koff Fus3pTpY Dig1Koff Fus3pTpY Dig2
Koff Fus3pTpY Far1Koff Fus3pY Dig1Koff Fus3pY Dig2
Koff Fus3pY Far1Koff Gpa1GDP Ste4Ste18Koff Gpa1GTP Ste4Ste18
Koff Kss1pT Dig1Koff Kss1pT Dig2Koff Kss1pT Far1
Koff Kss1pTpY Dig1Koff Kss1pTpY Dig2Koff Kss1pTpY Far1
Koff Kss1pY Dig1Koff Kss1pY Dig2Koff Kss1pY Far1
Koff MAPKpT Sst2Koff MAPKpT Ste11Koff MAPKpTpY Sst2
Koff MAPKpTpY Ste11Koff MAPKpY Sst2Koff MAPKpY Ste11
Koff Msg5 MAPKKoff Pheromone Ste2Koff Ptp MAPK
Koff Ste12Dig1 Dig2Koff Ste12Dig1 Dig2PO4Koff Ste12Dig1 Fus3
Koff Ste12Dig1 Fus3pTKoff Ste12Dig1 Fus3pTpYKoff Ste12Dig1 Fus3pY
Koff Ste12Dig1 Kss1Koff Ste12Dig1 Kss1pTKoff Ste12Dig1 Kss1pTpY
Koff Ste12Dig1 Kss1pYKoff Ste12Dig2 Dig1Koff Ste12Dig2 Dig1PO4
Koff Ste12Fus3Dig2 Dig1Koff Ste12Fus3Dig2 Dig1PO4Koff Ste12Fus3 Dig1
Koff Ste12Fus3 Dig1PO4Koff Ste12Kss1Dig2 Dig1Koff Ste12Kss1Dig2 Dig1PO4
Koff Ste12Kss1 Dig1Koff Ste12Kss1 Dig1PO4Koff Ste12 Dig1
Koff Ste12 Dig1PO4Koff Ste12 Dig2Koff Ste12 Dig2PO4
Koff Ste12 Fus3Koff Ste12 Fus3pTKoff Ste12 Fus3pTpY
Koff Ste12 Fus3pYKoff Ste12 Kss1Koff Ste12 Kss1pT
Koff Ste12 Kss1pTpYKoff Ste12 Kss1pYKoff Ste2Gpa1GDP Ste4Ste18
Koff Ste2Gpa1GTP Ste4Ste18Koff Ste2 Gpa1Koff Ste2 Gpa1Ste4Ste18
Koff Ste2 Sst2Koff Ste2 YckKoff Ste4Ste18Ste5 Ste4Ste18Ste5
Koff Ste4Ste18Ste5 Ste5Koff Ste4Ste18 Ste4Ste18Ste5Ste5Koff Ste4Ste18 Ste5
Koff Ste4Ste18 Ste5Ste5Koff Ste4 Ste20Koff Ste5 Fus3
Koff Ste5 Kss1Koff Ste5 Ste11Koff Ste5 Ste5
Koff Ste5 Ste7Koff Ste7 MAPKKon Fus3pT Dig1
Kon Fus3pT Dig2Kon Fus3pT Far1Kon Fus3pTpY Dig1
Kon Fus3pTpY Dig2Kon Fus3pTpY Far1Kon Fus3pY Dig1
Kon Fus3pY Dig2Kon Fus3pY Far1Kon Gpa1GDP Ste4Ste18
Kon Gpa1GTP Ste4Ste18Kon Kss1pT Dig1Kon Kss1pT Dig2
Kon Kss1pT Far1Kon Kss1pTpY Dig1Kon Kss1pTpY Dig2
Kon Kss1pTpY Far1Kon Kss1pY Dig1Kon Kss1pY Dig2
Kon Kss1pY Far1Kon MAPKpT Sst2Kon MAPKpT Ste11
Kon MAPKpTpY Sst2Kon MAPKpTpY Ste11Kon MAPKpY Sst2
Kon MAPKpY Ste11Kon Msg5 MAPKKon Pheromone Ste2
Kon Ptp MAPKKon Ste12Dig1 Dig2Kon Ste12Dig1 Dig2PO4
Kon Ste12Dig1 Fus3Kon Ste12Dig1 Fus3pTKon Ste12Dig1 Fus3pTpY
Kon Ste12Dig1 Fus3pYKon Ste12Dig1 Kss1Kon Ste12Dig1 Kss1pT
Kon Ste12Dig1 Kss1pTpYKon Ste12Dig1 Kss1pYKon Ste12Dig2 Dig1
Kon Ste12Dig2 Dig1PO4Kon Ste12Fus3Dig2 Dig1Kon Ste12Fus3Dig2 Dig1PO4
Kon Ste12Fus3 Dig1Kon Ste12Fus3 Dig1PO4Kon Ste12Kss1Dig2 Dig1
Kon Ste12Kss1Dig2 Dig1PO4Kon Ste12Kss1 Dig1Kon Ste12Kss1 Dig1PO4
Kon Ste12 Dig1Kon Ste12 Dig1PO4Kon Ste12 Dig2
Kon Ste12 Dig2PO4Kon Ste12 Fus3Kon Ste12 Fus3pT
Kon Ste12 Fus3pTpYKon Ste12 Fus3pYKon Ste12 Kss1
Kon Ste12 Kss1pTKon Ste12 Kss1pTpYKon Ste12 Kss1pY
Kon Ste2Gpa1GDP Ste4Ste18Kon Ste2Gpa1GTP Ste4Ste18Kon Ste2 Gpa1
Kon Ste2 Gpa1Ste4Ste18Kon Ste2 Sst2Kon Ste2 Yck
Kon Ste4Ste18Ste5 Ste4Ste18Ste5Kon Ste4Ste18Ste5 Ste5Kon Ste4Ste18 Ste4Ste18Ste5Ste5
Kon Ste4Ste18 Ste5Kon Ste4Ste18 Ste5Ste5Kon Ste4 Ste20
Kon Ste5 Fus3Kon Ste5 Kss1Kon Ste5 Ste11
Kon Ste5 Ste5Kon Ste5 Ste7Kon Ste7 MAPK
Kss1Kss1 numKss1 tot conc
Ksynth Gpa1Ksynth Sst2Ksynth Ste11
Ksynth Ste12 Dig2Ksynth Ste12 Far1Ksynth Ste12 Fus3
Ksynth Ste12 Gpa1Ksynth Ste12 Msg5Ksynth Ste12 Ptp
Ksynth Ste12 Sst2Ksynth Ste12 Ste12Ksynth Ste12 Ste2
Ksynth Ste2Ksynth Ste7
Late December 2006 MAPK pathway model - tmt
Localization effectsMAPKMAPK/phosphatase interactions
MAPK/target interaction propertiesMAPK pT only Kd factorMAPK pT only PO4 factor
MAPK pY only Kd factorMAPK pY only PO4 factorMAPK phosphorylation cascade
Main PageMain Page v2Major assumptions and points of contention
ModelExtension
Model Process page for 2007 04 22 12h14m39sModel Process page for 2007 07 03 16h24m59s
Model Process page for 2008 01 24 15h08m33s
Model Process page for 2008 01 24 15h08m33s (MAPK cascade model)Model Process page for 2008 01 24 15h08m33s (Receptor/G protein model)
Modeling tagsMoleculizerMsg5
Msg5 numMsg5 tot concMutants for fitting model
Naming, moving or deleting pagesNav bar
New Test page
Non-specific dephosphorylationOther yeast pathwaysParameter Estimation in Matlab
Parameter FittingPheromonePheromone-dependent cell cycle arrest
Pheromone/Receptor/G protein interactions
PheromoneWiki conventions
Pheromone tot conc
Protein dilution/synthesis due to cell growth
Ptp
Ptp2
Ptp2/3
Ptp2/Ptp3
Ptp3
Ptp numPtp tot concRGS(Sst2)/Galpha(Gpa1)/Receptor(Ste2) interactions
RGS(Sst2) synthesis/degradation
Receptor
Receptor(Ste2) synthesis/endocytosis/degradation
STE2
STE5
Sandbox
Simple wiki editing examplesSst2Sst2 num
Sst2 synthesis/degradationSst2 tot concSte11
Ste11/Ste50 interactionsSte11 numSte11 pS only PO4 factor
Ste11 synthesis/degradationSte11 tot concSte12
Ste12 Dig1 Dig2 coop factorSte12 Dig1 Fus3 coop factorSte12 Dig1 Kss1 coop factor
Ste12 Dig1 PO4 factorSte12 Dig2 PO4 factorSte12 Fus3 pT factor
Ste12 Fus3 pTpY factorSte12 Fus3 pY factorSte12 Kss1 pT factor
Ste12 Kss1 pTpY factorSte12 Kss1 pY factorSte12 mediated protein synthesis
Ste12 numSte12 synthesis/degradationSte12 tot conc
Ste18
Ste2Ste2/Gpa1/Ste4:Ste18 binding rate constant constraints
Ste20Ste20 numSte20 tot conc
Ste2 Gpa1 Ste4Ste18 coop factorSte2 num
Ste2 synthesis/degradation
Ste2 synthesis/endocytosis/degradationSte2 tot concSte3
Ste4
Ste4/Ste18 interaction
Ste4/Ste20 interaction
Ste4/Ste5 interactions and Ste5 dimerization/oligomerization
Ste4:Ste18Ste4:Ste18/Ste20 interaction
Ste4:Ste18/Ste5 interactions and Ste5 dimerization/oligomerization
Ste4Ste18/Ste20 interaction
Ste4Ste18/Ste5 interactions and Ste5 dimerization/oligomerization
Ste4Ste18Ste5 Ste4Ste18Ste5 coop factorSte4Ste18Ste5 Ste5 coop factorSte4 num
Ste4 tot concSte5Ste5/MAPK cascade interactions
Ste50Ste50 numSte50 tot conc
Ste5 dimerization and Ste4 binding rate constant constraintsSte5 numSte5 tot conc
Ste7
Ste7/Fus3/Kss1 interactions
Ste7/MAPK interactions
Ste7 numSte7 pS only PO4 factorSte7 synthesis/degradation
Ste7 tot concTec1Tec1 synthesis/degradation
Tec1 totTest pageTimecourses for fitting model
Users
Why Join
Why join
Wiki conventions
Wiki parser
Yck
Yck1
Yck2
Yck3
Yck numYck tot concYeast pheromone response model
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