examples/activation-cases.json

[
  {"prompt": "Help me choose the best ESM workflow for this project.", "expected": "biohub-esm"},
  {"prompt": "Which ESM route should I use for a private 700-residue protein?", "expected": "biohub-esm"},
  {"prompt": "Which ESM workflow should I use instead of AlphaFold?", "expected": "biohub-esm"},
  {"prompt": "Check whether Biohub ESM is ready to use on this machine.", "expected": "biohub-esm-setup"},
  {"prompt": "Is Biohub ESM ready on this laptop?", "expected": "biohub-esm-setup"},
  {"prompt": "What might W43F do to GB1?", "expected": "esmc"},
  {"prompt": "Could W43F change how GB1 behaves?", "expected": "esmc"},
  {"prompt": "Calculate entropy for this protein sequence.", "expected": "esmc"},
  {"prompt": "Extract hidden states for this amino-acid sequence.", "expected": "esmc"},
  {"prompt": "Where should I explore mutations in PETase?", "expected": "esmc"},
  {"prompt": "What patterns does ESMC see in ATP synthase, and where do they appear on its structure?", "expected": "esmc"},
  {"prompt": "Map the mutational landscape of PETase and show me where it is most constrained or tolerant.", "expected": "esmc"},
  {"prompt": "Show me what ESMC has learned about ATP synthase and map the strongest features onto its structure.", "expected": "esmc"},
  {"prompt": "Show me what GB1 looks like.", "expected": "esmfold2"},
  {"prompt": "Could you display the 3D structure of GB1?", "expected": "esmfold2"},
  {"prompt": "Fold this protein sequence.", "expected": "esmfold2"},
  {"prompt": "Compare ESM protein folding with AlphaFold.", "expected": "esmfold2"},
  {"prompt": "Show me how RNase H1 engages its RNA-DNA hybrid.", "expected": "esmfold2"},
  {"prompt": "Fold ubiquitin with my A3M and show me the structure and confidence.", "expected": "esmfold2"},
  {"prompt": "Model how a modified GLP-1 peptide with a lipid linker might engage GLP-1R, then show me the complex.", "expected": "esmfold2"},
  {"prompt": "Use my paired MSAs to model an antibody-antigen complex.", "expected": "esmfold2"},
  {"prompt": "Find proteins similar to GB1.", "expected": "esm-atlas"},
  {"prompt": "Which proteins are the nearest neighbors of GB1?", "expected": "esm-atlas"},
  {"prompt": "Plan a binder-design campaign for GB1.", "expected": "esmfold2-binder-design"},
  {"prompt": "Sketch out a minibinder design campaign against GB1.", "expected": "esmfold2-binder-design"},
  {"prompt": "Use Clustal Omega to align these sequences.", "expected": null},
  {"prompt": "Convert this A3M alignment to FASTA.", "expected": null},
  {"prompt": "What is an RNA-DNA hybrid?", "expected": null},
  {"prompt": "How are lipid linkers synthesized?", "expected": null},
  {"prompt": "Explain paired MSAs.", "expected": null},
  {"prompt": "Run AlphaFold3 on this complex.", "expected": null},
  {"prompt": "Use Boltz to dock this ligand.", "expected": null},
  {"prompt": "Open this experimentally determined PDB in the Molecular Structure Viewer without running ESM.", "expected": null},
  {"prompt": "Show me what California looks like on a road atlas.", "expected": null},
  {"prompt": "What might W43F do to a circuit?", "expected": null},
  {"prompt": "Find books similar to GB1.", "expected": null},
  {"prompt": "Fold this paper in half.", "expected": null},
  {"prompt": "Calculate the Shannon entropy of this probability distribution.", "expected": null},
  {"prompt": "Inspect hidden states in this language model.", "expected": null},
  {"prompt": "Show me the logits for this text classifier.", "expected": null},
  {"prompt": "Create an embedding for this text sequence.", "expected": null},
  {"prompt": "Design a marketing campaign for a three-ring binder.", "expected": null},
  {"prompt": "Analyze PTM sites in this phosphoproteomics dataset.", "expected": null},
  {"prompt": "Route this workload to compute.", "expected": null},
  {"prompt": "Help me choose a machine-learning workflow for this project.", "expected": null},
  {"prompt": "Fine-tune GPT for customer support.", "expected": null}
]