• 0. IMPORTANT
    • 0.1 General
    • 0.2 Notation
  • 1. Enzyme Family Background
    • 1.1 Classification
    • 1.2 Reaction chemistry
    • 1.3 Substrate scope terminology
    • 1.4 Why substrate specificity is structurally interesting
  • 2. Structural Information
    • 2.1 Experimental structures for reference
    • 2.2 AlphaFold model for Cn PhaC1
    • 2.3 Key structural regions (Cn PhaC1 numbering)
    • 2.4 Substrate-binding tunnel residues
    • 2.5 Tunnel geometry notes
  • 3. Dataset Scope, Limitations, and Compensating Strategies
    • 3.1 What your dataset contains
    • 3.2 Implications and honest limitations
    • 3.3 What this dataset IS good for
    • 3.4 Compensating strategies
    • 3.5 Class II reference comparison
  • 4. Experimental Mutation Database
    • 4.1 Key literature to mine for Cn PhaC1 mutations
    • 4.2 Gain-of-function mutations (change in substrate specificity or activity)
    • 4.3 Neutral mutations (no significant effect on specificity)
    • 4.4 Deleterious mutations (loss of activity or expression)
    • 4.5 Combinatorial / double mutants
    • 4.6 Thermostability mutations
    • 4.7 Positions that have NOT been mutated in literature
    • 4.8 Data quality notes
  • 5. Your Starting Enzyme (Wild-Type Cn PhaC1)
    • 5.1 Identity
    • 5.2 Known properties of WT Cn PhaC1
    • 5.3 Full WT sequence
    • 5.4 Substrate-binding pocket region
    • 5.5 Catalytic and key residue positions (for quick reference)
  • 6. Engineering Target
    • 6.1 Primary goal
    • 6.2 Secondary goals
    • 6.3 Acceptable tradeoffs
    • 6.4 Hard constraints — DO NOT VIOLATE
    • 6.5 What has already been tested
  • 7. Production and Assay Context
    • 7.1 Expression system
    • 7.2 Eventual In vivo PHA production conditions
    • 7.3 In vitro activity assay (if used)
    • 7.4 PHA analysis
  • 8. Reasoning Guidelines for LLM
    • 8.1 Dataset context — tell the LLM explicitly at session start
    • 8.2 Prioritization criteria (in order, adjusted for this dataset)
    • 8.3 Required output format for mutation suggestions
    • 8.4 Reasoning I do NOT want
    • 8.5 Especially useful prompts for this dataset type
    • 8.6 My background
  • 9. Session Log
    • Session [DATE]
    • Session [DATE]
  • 10. Experimental Results Log
    • Experiment [DATE / ID]
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