VCell Node Rate Constants

[Ethan John]

Hello,

     I am an undergraduate student working in a research lab utilizing VCell to model intracellular protein interactions. However, I am having trouble finding specific forward and reverse rate constants for these mass-action reactions as these are required to formulate any simulation results. Literature searches seem to be limited by various factors that prevent specific values from being extracted. Would you recommend searching through the VCell database for similar published models and using/referencing their constants? Or is it more typical for VCell users to test estimated constants through a trial-and-error process? If there are any other methods you would recommend I would really appreciate it.

Thank you very much.

[Blinov,Michael]

Hello, 

There are several methods to find appropriate rate constants, but there are no best approaches. You always end up with a trial-and-error process.

• Search for similar models in the BioModels database https://www.ebi.ac.uk/biomodels/,  they also have parameters search https://www.ebi.ac.uk/biomodels/parameterSearch
• Search for similar models in VCell database, and check rate constants there.
• Search BioNumbers  https://bionumbers.hms.harvard.edu/search.aspx and SABIO-RK (http://sabio.h-its.org/) databases.
• Use parameter estimation in VCell to fit rate constants to approximate time curves for just a single reaction.
  

Good luck, you got to the most complicated part of modeling!

Best,

Michael

• 
  
  
  

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From: vcell-...@googlegroups.com <vcell-...@googlegroups.com> on behalf of Ethan John <ethang...@gmail.com>
Sent: Tuesday, November 7, 2023 11:31 AM
To: VCell Open Discussion Forum <vcell-...@googlegroups.com>
Subject: [VCell] VCell Node Rate Constants

 

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Hello,

     I am an undergraduate student working in a research lab utilizing VCell to model intracellular protein interactions. However, I am having trouble finding specific forward and reverse rate constants for these mass-action reactions as these are required to formulate any simulation results. Literature searches seem to be limited by various factors that prevent specific values from being extracted. Would you recommend searching through the VCell database for similar published models and using/referencing their constants? Or is it more typical for VCell users to test estimated constants through a trial-and-error process? If there are any other methods you would recommend I would really appreciate it.

Thank you very much.

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