bio-retrosynthesis
Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Transformer), and disconnection-aware multi-objective search (MO-MCTS). Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.
npx skills add BioTender-max/awesome-bio-agent-skills --skill retrosynthesis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: AiZynthFinder 4.4+, Chemformer 1.3+, RDKit 2024.09+, RDChiral 1.1+, Aizynthtrain 1.0+, ASKCOS Lite 0.5+. Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `aizynthcli --version` If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Retrosynthesis Plan synthetic routes from a target molecule back to commercially-available building blocks. AiZynthFinder 4.0 (Saigiridharan, Hassen, Lai, Torren-Peraire, Engkvist, Genheden 2024 *J Cheminform* 16:57, AstraZeneca) is the open-source production-grade tool: Monte Carlo Tree Search (MCTS) + template-based expansion + multi-objective scoring (MO-MCTS). Chemformer (Irwin 2022) is template-free transformer alternative. ASKCOS (MIT) is the academic reference. Modern best practice combines retrosynthesis with **forward validation** (the predicted route should also predict the target from starting materials via Molecular Transformer) and building-block availability (eMol
- Version Compatibility
- Retrosynthesis Method Taxonomy
- Decision Tree by Scenario
- AiZynthFinder Setup
- Route Output Analysis
- Route Scoring (MO-MCTS)
- Building Block Stocks
- Forward Validation with Molecular Transformer
- Template-Free with Chemformer
- Disconnection-Aware Design (DAD)
- Cost-Aware Synthesis
- Per-Tool Failure Modes
- AiZynthFinder -- template coverage gap
- Chemformer -- non-canonical SMILES output
aizynthtrain build-stock --input zinc_building_blocks.smi --output zinc.h5 aizynthcli --smiles compounds.smi --output routes.json \
What does the bio-retrosynthesis skill do?
Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Transformer), and disconnection-aware multi-objective search (MO-MCTS). Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill retrosynthesis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.