eQuilibrator - the biochemical thermodynamics calculator

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Contents:

• About Us
  • About eQuilibrator
  • Implementation of eQuilibrator
  • Acknowledgements
  • References
• eQuilibrator Classic Reactions
  • Energy Currency and ATP Hydrolysis
  • Thioester Bonds are Energetic Too
  • The Oxidation of Glucose
  • Plants Make Glucose from CO₂
  • Glycolysis and Fermentation
    • NADH as an Electron Carrier
    • Ethanol Fermentation
    • Mixtures of Fermentation Products
    • Glycolysis in Gory Detail
  • Respiration
    • Alternative Respiratory Pathways
  • Transamination for Making Amino Acids
  • Metabolism of Alkanes and Fatty Acids
    • Example of Octane Breakdown
    • Energy Balance in Octane Breakdown
    • Fatty Acid Metabolism
  • The TCA Cycle
    • Metabolism of Acetyl-CoA
    • Constructing the TCA Cycle
    • Oxaloacetate back to α-Ketoglutarate
    • Anaplerotic Reactions
    • pH Dependence
  • References
• Pathway Analysis
  • Overview of Pathway Analysis
  • Using eQuilibrator to profile your pathway
    • 1. Generating an SBtab model of your pathway
    • 2. Verifying and editing the model
    • 3. Performing pathway analysis
  • Max-min Driving Force
  • Enzyme Cost Minimization
  • References
• Frequently Asked Questions
  • How do I search for a compound or enzyme?
  • How do I search for a reaction?
  • What are “standard conditions?”
  • What are Δ_rG°, Δ_rG’° and Δ_rG’?
  • What are Δ_fG’ and Δ_fG’°?
  • What does the ‘m’ in Δ_rG’^m, Δ_fG’^m, and E’^m mean?
  • Why is Δ_rG “not available?”
  • How do you calculate the uncertainty for each estimation?
  • How do you deal with gases like O₂ and H₂?
  • Why can’t I change the concentration of H⁺ ions?
  • Why can’t I change the concentration of water?
  • Why can’t I change the temperature?
  • What are CO₂(aq) and CO₂(total)?
  • What are “half-reactions?””
  • What’s so complicated about redox reactions involving iron?
  • Why is the value for ATP hydrolysis different than some textbooks?
  • What is the total driving force of a pathway?
  • What is the MDF of a pathway?
  • What is the ECM of a pathway?
  • How can I contact the people behind eQuilibrator?
  • References
• Relevant publications
• What’s new …
  • in eQuilibrator 3.0?
  • in eQuilibrator 2.2?
  • in eQuilibrator 2.1?