Literature Reaction Similarity Search

Overview

Search local reaction examples by template, named reaction, functional handles, and ORD-compatible fields. It is in the AI Synthesis category and is intended to support route ideation, reaction prediction, context recommendation, and synthesis risk review.

When To Use It

• You need a focused workflow for literature reaction similarity search without leaving ChemistryAtlas.
• You want a result that can be saved, shared, or chained into another chemistry app.
• You want the calculation assumptions and limitations visible next to the output.

Inputs

• text - Chemistry input - type: textarea - Use formulas, names, SMILES-like text, reactions, or key=value options. Heavier engines will plug into this same app surface.

Recommended Workflow

• Enter targets, reactants, products, or conditions; review ranked routes or predicted outcomes; then validate against literature, availability, safety, and your lab's capabilities.
• Start with the smallest representative input, confirm the parser understood it, then scale to a larger list or workflow.
• Save the generated report when the result will feed a notebook entry, route review, model comparison, or team discussion.

Outputs

• A Markdown-style chemistry report with parsed inputs, assumptions, and calculated or predicted results.
• Structured tables when the app returns multiple compounds, reagents, routes, peaks, candidates, or model rows.
• Warnings, fallback notes, and sidecar availability messages when a specialized engine is not installed or not reachable.

Method And Backend Notes

This app has a runnable ChemistryAtlas backend path. Backend type: database. ChemistryAtlas roadmap MVP: runnable report now; specialist cheminformatics/model backend plugs into this app surface next. When ASKCOS/RDChiral/RDCanon sidecars are available, this app can use them; otherwise it keeps a deterministic local report surface so chemists can still triage inputs.

How To Interpret Results

• AI synthesis output is a hypothesis generator. A route is useful only after a chemist checks selectivity, workup, purification, hazards, and precedent.
• Compare results across related molecules, controls, blanks, literature examples, or known reactions whenever possible.
• For decisions that affect safety, synthesis scale-up, biological testing, purchasing, or publication, verify with primary data and expert review.

Example Input

reaction=CC(=O)O.NC>>CC(=O)NC
reaction_type=amide

Common Checks Before Acting

• Confirm names, salts, stereochemistry, tautomers, protonation state, and hydration state.
• Check units, concentrations, equivalent definitions, and significant figures.
• Record external database versions, model versions, sidecar availability, and any manual edits made after the app output.

Related Apps

• Reaction Template Explorer (reaction-template-explorer)
• Forward Reaction Predictor Pro (forward-reaction-predictor-pro)
• Retrosynthesis Planner Pro (retrosynthesis-planner-pro)
• Reaction Context Recommender (reaction-context-recommender)
• Impurity / Side Product Predictor (impurity-side-product-predictor)

Acknowledgements And Validation

• ChemistryAtlas documentation and UI were prepared for chemistry discovery workflows.
• Where available, calculations may use open-source cheminformatics, reaction-informatics, spectra, docking, or machine-learning engines such as RDKit-family tooling, ASKCOS-style sidecars, ChemProp, ms-pred/ICEBERG, PyScreener, and MolPAL.
• Always verify important results against primary literature, official SDS records, instrument software, validated models, and local laboratory procedures.