Example Prompts

Now that you’re connected, you can start asking questions about the scientific tools SandboxAQ provides. A good first prompt is:

What tools do you have available from SandboxAQ?

The examples below are copy-paste ready prompts for exploring AQPotency (small-molecule potency, selectivity, and target scanning) and AQCat (catalysis and surface adsorption). Swap in your own SMILES, UniProt IDs, or surfaces as needed.

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AQPotency prompts

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Predict binding potency against a single target with AqpotencyPotency

Predict the binding potency of CC1=CC=C(C=C1)S(=O)(=O)N against protein P00533.

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Scan a compound against a protein panel with AqpotencyScan

Scan CC1=CC=C(C=C1)S(=O)(=O)N against the human_kinome.

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Assess selectivity against off-targets with AqpotencySelectivity

Assess the selectivity of CC1=CC=C(C=C1)S(=O)(=O)N against target Q15078 vs. off-targets Q6J9G0, Q13546, Q15768.

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Rank a focused library with AqpotencyScreen

I have a focused library of ~1,000 compounds. Upload the file, then use the AqpotencyScreen tool to rank the top 25 compounds by predicted potency against UniProt P00533 (EGFR) so I can shortlist them for docking. Include ligand_similarity and protein_in_training on each row.

Download Example CSV

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Profile a series with AqpotencySelectivity

For the SMILES below, use the AqpotencySelectivity tool with target_uniprot_id='P50613' (CDK7) and off_target_uniprot_ids=['P06493','P24941','P11802','Q00534','P50750'] (CDK1, CDK2, CDK4, CDK6, CDK9). Return per-off-target fold selectivity and the strongest-off-target summary.

CN(C)CCN(Cc1ccccc1)c1ccccn1
CN(C)CCN(Cc1cccs1)c1ccccn1
CN(C)CCN1C(=O)c2ccccc2N(C)c2ccccc21
CN(C)CCOC(=O)C(c1ccccc1)C1(O)CCCC1
CN(C)CCOC(C)(c1ccccc1)c1ccc(Cl)cc1
CN(C)CCOC(C)(c1ccccc1)c1ccccn1
CN(C)CCOC(c1ccc(Cl)cc1)c1ccccn1
CN(C)CCOC(c1ccccc1)c1ccc(Br)cc1
CN(C)CCOC(c1ccccc1)c1ccccc1
CN(C)CCOc1ccc(/C(=C(/CCCl)c2ccccc2)c2ccccc2)cc1
CN(C)CC[C@@H](c1ccc(Br)cc1)c1ccccn1
CN(C)CC[C@@H](c1ccc(Cl)cc1)c1ccccn1

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AQCat prompts

Each prompt below is documented in full — with the parameters your client sends and representative output — on the AQCat Adsorption Spin page.

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Find the lowest-energy adsorption configuration

Use the AQCat tool to find the lowest-binding-energy configuration for N₂ adsorbed on a cobalt-nickel (111) surface. Report the binding energy of the winning placement and confirm whether the relaxation converged.

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CO oxidation on Cu(110)

For a CO oxidation catalysis study, use the AQCat tool to find the most favorable adsorption configuration for CO on a copper (110) surface. Report the binding energy of the winning placement and how many placements relaxed to convergence.

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Compare H adsorption across Fe facets

For a hydrogen evolution research question, use the AQCat tool to compare atomic hydrogen (H) adsorption across three iron surfaces — Fe (100), Fe (110), and Fe (111). Make one AQCat call per facet, then report the binding energy and convergence status for each, and identify which facet binds H most strongly.

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Rank a copper alloy series by CO binding energy

For a CO oxidation screen, use the AQCat tool to rank four copper-based compositions — Cu, Cu-Zn, Cu-Ni, and Cu-Pd — by CO binding energy on the (111) facet. Make one AQCat call per composition, then report the binding energy and convergence status for each and rank them from strongest to weakest binding.

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Check whether spin polarization applies

Use the AQCat tool to compute the binding energy of atomic nitrogen (N) on an iron (110) surface and on a platinum (111) surface. Report the is_spin_off flag for each alongside the binding energy, and tell me whether the two results can be compared to each other.