AiZynthFinder quickstart

You want to plan a synthetic route for a target molecule: paste a single target SMILES, choose your stock sources and template policy, and submit — five steps from a sanitized SMILES to downloadable, scored routes that tell you whether the target is synthetically accessible from commercial starting materials.

About AiZynthFinder

AiZynthFinder is developed by the AstraZeneca Molecular AI team and is one of the leading open-source retrosynthesis planning tools. Version 4.0, published in the Journal of Cheminformatics in May 2024, introduced filter policies and bonds-to-freeze constraints for more controlled route generation.

In published benchmarks, AiZynthFinder achieves an 80–86% success rate for finding routes where all starting materials are commercially available.

Prerequisites

• AiZynthFinder enabled in your workspace.
• A single target SMILES; ensure it is sanitized, neutralized, and free of disconnected salt fragments.
• At least one stock source selected (public or in-house) — routes are only marked purchasable when every starting material exists in a selected stock.

Steps

1. Open the AiZynthFinder tool and start a new job.
2. Enter the target SMILES directly, or use From Previous Job to pull a compound from a REINVENT, GenMol, or database-search result.
3. Choose your stocks (for example zinc) and expansion policy (uspto_50k is a good default), and leave search breadth and depth at their defaults to start.
4. Submit and monitor the job log; transient failures retry automatically. A typical search runs 5–30 minutes depending on molecule complexity.
5. Download routes (JSON/CSV) and review the score, step count, and purchasability flag for each.

Reading the first result

• Score (0.0–1.0): higher is a more likely route; treat > 0.8 as high-confidence.
• Purchasable: filter for is_purchasable: true routes first — those need no custom intermediate synthesis.
• Length: fewer steps is generally preferable for the same score.

The result also renders as an interactive retrosynthetic tree on the canvas, with green nodes for in-stock building blocks, yellow for orderable, and red for materials needing custom synthesis. See outputs & interpretation for the full field reference.

Quick checks

• Confirm the job metadata lists the expected stock set and policy.
• Ensure at least one route is marked purchasable; if none are, revisit your stock choices before concluding the target is inaccessible.
• Save the job URL alongside project notes for reproducibility.

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