---
title: Which tool?
description: >-
  Match a scientific goal to the tool or workflow that answers it — grouped by
  stage of the discovery pipeline.
tags:
  - orientation
  - tools
  - workflows
---

Find your goal in the tables below. Each row names the tool to run and, where one exists, the [passport](/docs/passports-explained) 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](/docs/how-orchestration-works). 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](/docs/capabilities) explains the difference and when to pick which.

## Structure

| Your goal | Run | One-shot pipeline |
|---|---|---|
| Predict 3D structure from a sequence | [ESMFold](/docs/esmfold) | — |
| Predict structure from a UniProt ID | [AlphaFold](/docs/alphafold) | — |
| Work with an experimental structure | [PDB lookup](/docs/pdb) | — |
| Design or reason over sequences | [ESM3](/docs/esm3) | — |
| Search for similar sequences | [BLAST](/docs/blast) | — |

## Binding and docking

| Your goal | Run | One-shot pipeline |
|---|---|---|
| Find binding pockets on a target | [P2Rank](/docs/p2rank) | — |
| Dock a small molecule to a target | [DiffDock](/docs/diffdock) | — |
| Minimize a docked complex and get its energy (**not** a binding affinity) | [MM-GBSA](/docs/mmgbsa) | — |

## ADMET and safety

| Your goal | Run | One-shot pipeline |
|---|---|---|
| Predict ADMET / pharmacokinetics | [ADMET-AI](/docs/admet-ai) | — |
| Predict solubility | [DeepSol](/docs/deepsol), [GraphSol](/docs/graphsol) | — |
| Predict toxicity | [ADMET-AI](/docs/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](/docs/passports/safety) | — |

## Generative design and synthesis

| Your goal | Run | One-shot pipeline |
|---|---|---|
| Propose new molecules | [REINVENT4](/docs/reinvent), [GenMol](/docs/genmol) | — |
| Grow or decorate a fragment | [GenMol](/docs/genmol) (scaffold decoration, motif extension) | — |
| Plan a synthesis route | [AiZynthFinder](/docs/aizynthfinder) | — |
| Handle SMILES and reactions | [RDKit](/docs/rdkit), [RxnFP](/docs/rxnfp) | — |

## Databases and literature

| Your goal | Run | One-shot pipeline |
|---|---|---|
| Search bioactive compounds | [ChEMBL](/docs/chembl), [PubChem](/docs/pubchem) | — |
| Find purchasable compounds | [ZINC](/docs/zinc) | — |
| Search protein annotations | [UniProt](/docs/uniprot) | — |
| Mine literature and entities | [PubMed](/docs/pubmed), [BioBERT](/docs/biobert) | [Literature passport](/docs/passports/literature) |
| Find clinical trials | [Clinical trials](/docs/clinical-trials) | — |

## Target discovery and profiles

| Your goal | Run | One-shot pipeline |
|---|---|---|
| Go from disease to druggable target | [Genomics](/docs/genomics), [causal genomics](/docs/causal-genomics) | — |
| Profile a compound end-to-end | [Compound passport](/docs/passports/compound) | — |
| Profile a target end-to-end | [Target passport](/docs/passports/target) | — |
| Map a therapeutic area | [Therapeutic Area passport](/docs/passports/therapeutic-area) | — |

## Crystal structure and XRD

| Your goal | Run | One-shot pipeline |
|---|---|---|
| Analyze a powder XRD pattern | [PyWPEM](/docs/pywpem) | — |
| Search reference powder patterns | [OpXRD](/docs/opxrd) | — |
| Predict a small-molecule crystal structure | [XTalNet](/docs/xtalnet) | — |

> **Chaining tools yourself**

> These are entry points, not fences — most tools feed the next. To see the documented multi-tool sequences (virtual screening, lead optimization, safety assessment), see [Workflows](/docs/workflows). To run a chain from a script, see the [CLI](/docs/cli).