AiZynthFinder route review guide

This page lets you triage the routes AiZynthFinder returns — first-pass filtering on purchasability and step count, realism checks on disconnections, interpreting route scores, and comparing runs. Purchasability and step count most affect which routes are worth handing off, so lead with those before weighing scores.

First-pass filters

• Prioritize routes with is_purchasable true and minimal num_steps.
• Remove routes relying on intermediates that lack stock hits or look unstable.
• Prefer higher score only when routes are also stock-feasible.

Realism checks

• Inspect template IDs to spot unlikely disconnections; down-rank brittle steps.
• Watch for protecting-group heavy paths that inflate steps without adding value.
• Confirm reagents are in-stock and not specialty-only items if speed matters.
• Review filter policy outputs if using v4.0 filter policies to understand why certain reactions were rejected.

Understanding route scores

AiZynthFinder's scoring reflects template probabilities accumulated across all reaction steps. In published benchmarks, the tool achieves 80-86% success rates for finding routes with commercially available starting materials. When evaluating routes:

• High scores (>0.8): Strong template confidence at each step; prioritize these routes.
• Moderate scores (0.6-0.8): Some steps have lower template confidence; verify reaction feasibility manually.
• Low scores (<0.6): May include speculative disconnections; use as backup options only.

Consider the search algorithm used (MCTS, Nested Monte Carlo, or Greedy Best First) when comparing runs, as different algorithms may prioritize routes differently.

Comparing routes

• Compare only runs with matching stock sets, policy, and search limits.
• Keep 2–4 top candidates: one shortest route, one highest score, one backup with diversified steps.
• Note any manual tweaks you would apply (e.g., swap a late-stage disconnection) for CRO handoff.

Handing off

• Share CSV summary plus the purchasable subset for CRO quotes.
• Attach Routes JSON for teams that want full intermediate detail.
• Log the job URL and chosen configuration in tickets/ELN for reproducibility.