Which tool?
Match a scientific goal to the tool or workflow that answers it — grouped by stage of the discovery pipeline.
Find your goal in the tables below. Each row names the tool to run and, where one exists, the passport that profiles the whole subject in one pass.
To run a chain, describe the whole goal and the orchestrator links the tools for you — see How the orchestrator picks tools. Run the tools one by one when you need to tune a step or inspect intermediates.
Where a goal lists more than one tool, they do roughly the same thing — What you can achieve explains the difference and when to pick which.
Structure
| Your goal | Run | One-shot pipeline |
|---|---|---|
| Predict 3D structure from a sequence | ESMFold | — |
| Predict structure from a UniProt ID | AlphaFold | — |
| Work with an experimental structure | PDB lookup | — |
| Design or reason over sequences | ESM3 | — |
| Search for similar sequences | BLAST | — |
Binding and docking
| Your goal | Run | One-shot pipeline |
|---|---|---|
| Find binding pockets on a target | P2Rank | — |
| Dock a small molecule to a target | DiffDock | — |
| Minimize a docked complex and get its energy (not a binding affinity) | MM-GBSA | — |
ADMET and safety
| Your goal | Run | One-shot pipeline |
|---|---|---|
| Predict ADMET / pharmacokinetics | ADMET-AI | — |
| Predict solubility | DeepSol, GraphSol | — |
| Predict toxicity | ADMET-AI (DILI, hERG, AMES, ClinTox, Tox21, CYP inhibition) or safety_classify (structural alerts); acute-toxicity class and organ toxicity have no replacement | — |
| Assess a marketed drug's safety | Safety passport | — |
Generative design and synthesis
| Your goal | Run | One-shot pipeline |
|---|---|---|
| Propose new molecules | REINVENT4, GenMol | — |
| Grow or decorate a fragment | GenMol (scaffold decoration, motif extension) | — |
| Plan a synthesis route | AiZynthFinder | — |
| Handle SMILES and reactions | RDKit, RxnFP | — |
Databases and literature
| Your goal | Run | One-shot pipeline |
|---|---|---|
| Search bioactive compounds | ChEMBL, PubChem | — |
| Find purchasable compounds | ZINC | — |
| Search protein annotations | UniProt | — |
| Mine literature and entities | PubMed, BioBERT | Literature passport |
| Find clinical trials | Clinical trials | — |
Target discovery and profiles
| Your goal | Run | One-shot pipeline |
|---|---|---|
| Go from disease to druggable target | Genomics, causal genomics | — |
| Profile a compound end-to-end | Compound passport | — |
| Profile a target end-to-end | Target passport | — |
| Map a therapeutic area | Therapeutic Area passport | — |
Crystal structure and XRD
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