---
title: What you can achieve
description: >-
  Start from the outcome, not the tool. Most goals are served by more than one
  tool that does roughly the same thing — here's the capability and which tool
  fits.
tags:
  - orientation
  - capabilities
  - concepts
---

Pick the outcome you need; the note under it names the tool that fits. Most outcomes have **more than one tool**, differing in speed, coverage, or the input they take.

When you describe a goal in [chat](/docs/chat), the orchestrator makes this choice for you. This page is the map behind that choice.

## Structure

### Predict a protein's 3D structure
Get atomic coordinates for a protein you can't look up.

- [AlphaFold](/docs/alphafold) — **fetches** a pre-computed structure by UniProt ID (seconds, no GPU). Try this first.
- [ESMFold](/docs/esmfold) — **predicts** from sequence. Use it for novel, engineered, or mutated sequences that aren't in a database.
- [PDB](/docs/pdb) — downloads an experimental structure (X-ray / cryo-EM / NMR) when one has been deposited — the highest-confidence option.
- [ESM3](/docs/esm3) — design and embeddings, not just folding.

**Pick:** in a database by UniProt ID → AlphaFold or PDB. Novel / mutant / engineered → ESMFold.

### Find where a drug could bind
- [P2Rank](/docs/p2rank) — detects and ranks druggable pockets on a structure. This is the entry step before docking.

## Binding and docking

Docking is a **three-step capability**, not three interchangeable tools — run as much of the chain as your question needs.

1. [P2Rank](/docs/p2rank) — where is the pocket, and is it druggable?
2. [DiffDock](/docs/diffdock) — how does the ligand pose in it? (generates candidate poses)
3. [MM-GBSA](/docs/mmgbsa) — which pose is real? (physics-based binding-energy rescore)

**Pick:** pockets only → stop at P2Rank. Poses → DiffDock. Confident ranking → add MM-GBSA. Ask for the whole chain in one request and the orchestrator runs the steps in order.

## ADMET and safety

### Predict ADMET (absorption, distribution, metabolism, excretion, toxicity)
- [ADMET-AI](/docs/admet-ai) — a broad panel, fast. Best for early screening and library triage.
- [DeepPurpose](/docs/deeppurpose) — narrower: predicts drug–target interaction scores for the targets you supply — reach for it for selectivity and off-target questions.
- [RDKit](/docs/rdkit) — descriptors and drug-likeness filters only (Lipinski, PAINS) — fast, deterministic, no ML.

**Pick:** broad screen → ADMET-AI. Off-target panel → DeepPurpose. Just drug-likeness flags → RDKit.

### Predict solubility
- [DeepSol](/docs/deepsol) and [GraphSol](/docs/graphsol) predict solubility by different methods — run both for a consensus.

### Predict toxicity
- [ADMET-AI](/docs/admet-ai) covers DILI, hERG, AMES, ClinTox, Tox21 and CYP inhibition; `safety_classify` covers structural alerts. Acute-toxicity class and organ toxicity are no longer predicted by any tool.

## Chemistry

### Search for compounds
- [ChEMBL](/docs/chembl) — bioactivity and medicinal-chemistry data; start here when you know the target.
- [PubChem](/docs/pubchem) — search by structure, similarity, or property.
- [ZINC](/docs/zinc) — **purchasable** compounds and their vendor catalog codes; reach for it when procurement matters.

**Pick:** know the target → ChEMBL. Search by structure → PubChem. Must be buyable → ZINC.

### Design new molecules
- [GenMol](/docs/genmol) — the preferred small-molecule generator.
- [REINVENT4](/docs/reinvent) — reinforcement-learning generation toward a target profile.

### Plan a synthesis and source building blocks
- [AiZynthFinder](/docs/aizynthfinder) — retrosynthetic routes; then [ZINC](/docs/zinc) to check which starting materials are purchasable.

## Genomics and omics

### Analyze single-cell data
- [Scanpy](/docs/scanpy) — classical, fast, interpretable clustering and differential expression.
- [scvi-tools](/docs/scvi-tools) — deep generative models; reach for it for batch correction and unknown cell types.

**Pick:** speed and interpretability → Scanpy. Batch effects / novel cell types → scvi-tools.

### Go from disease to target
- [Genomics](/docs/genomics) and [causal genomics](/docs/causal-genomics) form the expression → differential → causal → druggable-target pipeline.

## Literature

### Mine papers and entities
- [PubMed](/docs/pubmed) and [BioBERT](/docs/biobert) — search literature and extract compound–target–disease relationships. For a packaged profile, generate a [Literature passport](/docs/passports/literature).

> **Two shortcuts**

> For a quick goal-to-tool lookup, use [Which tool?](/docs/which-tool). For a subject profiled across many of these capabilities at once, generate a [passport](/docs/passports-explained).