Retrosynthesis · Library Generation · Mechanistic Analysis

A Complete Chemistry Platform — Not Just Another Retrosynthesis Tool

Design at every level — retrosynthesis to reach a target, forward modules and AI property filters to find the right molecule, mechanistic analysis to catch by-products and design new reactions.

100,000+expert-coded reaction rules
700+functional-group conflicts checked per reaction
18,000+mechanistic, arrow-pushing transforms
3,000+protein targets for binding prediction

Not another literature-trained model

A hybrid, not a black box.

Most "AI for chemistry" tools learn what's likely from what's been published — and inherit every gap and bias in that record. Allchemy starts somewhere else: an expert-curated set of organic chemistry rules and heuristics that doesn't need a dataset to know a reaction is impossible.

  • No training corpus, at any point. Routes come from expert-encoded reaction rules and heuristics — not from mining precedent. There is no dataset to run out of, go stale, or be biased by.
  • Built-in negative data. Allchemy considers 700 incompatible functional-group combinations, encoded directly into the rule base, so the system rejects unrealistic chemistry instead of needing to learn to avoid it statistically.
  • Works on day one, on your target. No customer reaction history, no proprietary dataset, no warm-up period required to get a usable, explainable route.
  • AI layered on top, deliberately. Machine-learned models handle what they're genuinely good at — property prediction, protein-binding estimates, ADME/Tox scoring — while route feasibility stays governed by chemistry logic a chemist can inspect and trust.
  • Your data, only if you want it in. Allchemy doesn't need your reaction history to work — but if your team has proprietary data worth structuring, we can help digitize it for your own internal use.
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Proprietary datasets required to get a first route. Allchemy doesn't need to see your reaction history, your ELN, or a training corpus — the chemistry logic is already there, expert-curated, before your target ever comes in.

Allchemy manual retrosynthesis view, one disconnection back from the target, with reaction conditions and literature references shown for each option.
Fig. 1 — Manual retrosynthesis: one disconnection back from the target, with synthon options live platform view
Allchemy automated retrosynthesis result: a complete route tree generated end to end.
Fig. 1b — Automated retrosynthesis: a complete route tree, generated end to end

Chemistry first, at every level

Retrosynthesis, forward synthesis, mechanistic analysis, and property prediction.

Each mode runs on its own purpose-built rules. Chemistry first, throughout: every prediction is chemically meaningful, not just statistically likely.

Retrosynthesis

From a target back to buyable starting materials

Works back from a target to commercial or user-defined starting materials, ranking routes by cost, process fit, or green-chemistry metrics.

Search modes
  • Automated — returns ranked, complete pathways
  • Manual, step-by-step control
  • Dedicated logic for peptides
  • Rapid synthesizability assessment for large sets
Control & scale
  • Extensive control over reagents, constraints, and reaction scale — from lab bench to industrial multi-ton production
Forward modules · Library generation

From defined starting materials to everything reachable

  • Map the entire space of molecules makeable from your starting materials
  • Generate synthesizable analogs and bioisosteres of a lead
  • Modify a locked scaffold directly, without resynthesizing the core
  • Break a starting material down into smaller, valuable building blocks
Fine-grained · Mechanistic analysis

Finds the by-products other tools miss

Operates at the level of individual arrow-pushing steps rather than overall transformations — so instead of just predicting a main product, it traces exactly how by-products and side reactions form along the way.

By-product identification
  • 18,000+ encoded mechanistic, arrow-pushing transforms
  • Traces the exact step sequence that generates a by-product, not just the net reaction
  • Full by-product accounting alongside the main product, at every step
  • Supports process impurity analysis and forensic route tracing
AI · Property Prediction

Every molecule in Allchemy — including ones you introduce yourself — can be screened for binding, toxicity, and drug-likeness, and more.

  • Binding, toxicity, and drug-likeness scored on every molecule
  • ADME properties included alongside biological screening
  • 3,000+ protein targets screened automatically
  • Works on molecules you introduce yourself, not just ones Allchemy finds

What the hybrid core makes possible

Eight capabilities that fall out of building chemistry-first.

01

Deep reaction expertise

Tens of thousands of expert-coded reaction types, each checked against 700+ potentially conflicting functional groups.

02

Scale, by design

Reasons about industrial multi-ton processes as confidently as lab-bench ones — because scale-appropriateness is an encoded chemist rule, not something inferred from how much literature happens to exist at that scale.

03

By-product & process insight

Full by-product prediction from mechanistic, arrow-pushing steps — supporting process design and forensic route tracking.

04

Green chemistry scoring

Routes ranked on solvent and reagent hazard, atom economy, PMI, and other process-efficiency metrics.

05

Libraries that are actually makeable

Most compound libraries get generated first and checked for synthesizability later, if at all. Here the constraint is built in from the start — every molecule comes with a real route to make it.

06

Complexity, in every form

Stereo-rich small molecules, peptides, natural products — each carries its own kind of complexity, and each is handled on its own terms, not forced through one generic pipeline.

07

A chemist's foresight, encoded

Sometimes the smartest move doesn't look like progress yet. Allchemy can see far enough ahead to take it anyway.

08

Laboratory-validated

Predictions tested at bench and kilo-scale, with routes published in Nature, Science, and JACS — real-world proof that hand-encoded logic, not statistical fitting, produces chemistry that actually works.

Let's talk

See for yourself

Every company and academic group gets a free trial period to explore what Allchemy can do. Test it yourself — no curated examples, no script.

Peer-reviewed, not just demoed

Published research.

Our work appears in Nature, Science, JACS, and other leading journals.

Studying the outcomes and mechanisms of carbocationic rearrangements using algorithm-augmented experimentation
Gadina L. P. J.-L.; Baś S.; Makkawi A.; Bilgi-Gadina Y.; Klucznik T.; Beker W.; Grzybowski B. A. — 2026
Chem. Europe
mCLM: a modular chemical language model that generates functional and makeable molecules
Edwards C.; Han C.; Lee G.; Nguyen T.; Szymkuć S.; … Grzybowski B. A.; Burke M. D.; Ji H. — 2026
ICLR
Design and experimental validation of a photocatalyst recommender based on a large language model
Millward F.; Kulczykowski M.; Badland-Shaw J.; Szymkuć S.; … Grzybowski B. A.; Zysman-Colman E. — 2026
Angew. Chem.
Delocalized, asynchronous, closed-loop discovery of organic laser emitters
Strieth-Kalthoff F.; Hao H.; Rathore V.; Wołos A.; Roszak R.; … Grzybowski B. A. et al. — 2025
Science
Hierarchical reaction logic enables computational design of complex peptide syntheses
Molga K.; Beker W.; Roszak R.; Czerwiński A.; Grzybowski B. A. — 2025
JACS
Retro-forward synthesis design and experimental validation of potent structural analogs of known drugs
Makkawi A.; Beker W.; Wolos A.; Manna S.; Roszak R.; … Zadlo A.; Grzybowski B. A. — 2025
Chem. Sci.
Computer-generated, mechanistic networks assist in assigning the outcomes of complex multicomponent reactions
Krzeszewski M.; Vakuliuk O.; Tasior M.; Wołos A.; Roszak R.; … Grzybowski B. A.; Gryko D. T. — 2025
JACS
Sustainable production of chemicals by algorithm-assisted (bio)synthesis
Grzybowski B. A.; Żądło-Dobrowolska A.; Onishchenko N.; Larsen E. S. — 2025
Nat. Rev. Bioeng.
Artificial intelligence for retrosynthetic planning needs both data and expert knowledge
Strieth-Kalthoff F.; Szymkuć S.; Molga K.; Aspuru-Guzik A.; Glorius F.; Grzybowski B. A. — 2024
JACS
Systematic, computational discovery of multicomponent and one-pot reactions
Roszak R.; Gadina L.; Wołos A.; Makkawi A.; Mikulak-Klucznik B.; … Gryko D. T.; Grzybowski B. A. — 2024
Nat. Commun.
Estimation of multicomponent reactions' yields from networks of mechanistic steps
Szymkuć S.; Wołos A.; Roszak R.; Grzybowski B. A. — 2024
Nat. Commun.
Curtailing the scalable supply of fentanyl by using chemical AI
Mikulak-Klucznik B.; Klucznik T.; Beker W.; Moskal M.; Grzybowski B. A. — 2024
Chem
Computational synthesis design for controlled degradation and revalorization
Żądło-Dobrowolska A.; Molga K.; Kolodiazhna O. O.; Szymkuć S.; Moskal M.; Roszak R.; Grzybowski B. A. — 2024
Nat. Synthesis
Emergence of metabolic-like cycles in blockchain-orchestrated reaction networks
Roszak R.; Wołos A.; Benke M.; Gleń Ł.; Konka J.; Jensen P.; … Grzybowski B. A. — 2024
Chem
Computational prediction of complex cationic rearrangement outcomes
Klucznik T.; Syntrivanis L.-D.; Baś S.; Mikulak-Klucznik B.; Moskal M.; Szymkuć S.; … Grzybowski B. A. — 2023
Nature
Closed-loop optimization of general reaction conditions for heteroaryl Suzuki–Miyaura coupling
Angello N. H.; Rathore V.; Beker W.; Wołos A.; Jira E. R.; Roszak R.; … Burke M. D.; Grzybowski B. A. — 2022
Science
Computer-designed repurposing of chemical wastes into drugs
Wołos A.; Koszelewski D.; Roszak R.; Szymkuć S.; Moskal M.; Ostaszewski R.; … Grzybowski B. A. — 2022
Nature
Machine learning may sometimes simply capture literature popularity trends: heterocyclic Suzuki–Miyaura coupling
Beker W.; Roszak R.; Wołos A.; Angello N. H.; Rathore V.; Burke M. D.; Grzybowski B. A. — 2022
JACS
Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry
Wołos A.; Roszak R.; Żądło-Dobrowolska A.; Beker W.; Mikulak-Klucznik B.; … Szymkuć S.; Grzybowski B. A. — 2020
Science
Minimal-uncertainty prediction of general drug-likeness based on Bayesian neural networks
Beker W.; Wołos A.; Szymkuć S.; Grzybowski B. A. — 2020
Nat. Mach. Intell.
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For universities and research institutes

The AbSynth Collection.

Allchemy has curated and digitized over 3,000 classical total syntheses, comprising close to 60,000 individual steps — now freely available as a single reference file, the AbSynth Collection, for research institutions to use in their own analyses.

AbSynth Collection · Free for research use

3,000+ total syntheses, digitized

Decades of classical total-synthesis literature, expert-curated and digitized step by step — close to 60,000 individual steps in total, delivered as a single file, free for verified academic and research institutions.

  • 3,000+ total syntheses spanning classical synthetic literature
  • ~60,000 individual steps, digitized and structured
  • Delivered as a single reference file — no platform access required
  • Free for academic, research-institution, and allchemy.net use
How to cite

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Contact

Get in touch.

Whether you're from academia, industry, or a government agency — we'd love to discuss how Allchemy can support your work.

Platform demos and licensing
Academic and research collaborations
Government and classified environments
Press and media inquiries
Prefer email? Write to us directly at info@allchemy.net
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