# RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery

## TL;DR

RetroRules 2026 is an expanded database combining biochemical and organic reaction templates to improve pathway discovery and enzyme engineering.

## Contribution

The integration of organic chemistry reactions and improved template encoding enhances the database's scope and usability.

## Key findings

- RetroRules 2026 includes 1,174,216 templates from 92,698 reactions, covering 5796 fourth-level EC numbers.
- The database now supports mass-imbalanced reactions and uses RXNMapper for improved reaction mapping accuracy.
- A redesigned website and API allow multi-criteria exploration and data export in multiple formats.

## Abstract

RetroRules (https://retrorules.org) is an open resource of reaction templates, which are generic reaction representations that describe the atomic transformations underlying biochemical reactions. These templates are key to supporting metabolic pathway discovery, reaction prediction, and enzyme engineering. The 2026 release updates biochemical sources (MetaNetX, Rhea) and newly integrates organic chemistry reactions (USPTO), extending the scope of the database beyond enzymatic systems. The template encoding has been simplified by using implicit hydrogens and minimal atomic descriptors, resulting in faster and more compact representations. Radius range now spans 0–10, allowing finer control of reaction specificity. In addition, mass-imbalanced reactions are included, expanding the coverage of biochemically relevant transformations. Reaction mapping now relies on the transformer-based tool RXNMapper, improving accuracy. RetroRules 2026 comprises 1 174 216 templates derived from 92 698 reactions, covering 5796 fourth-level EC numbers. A redesigned website, updated Online Template Generator, and OpenAPI-defined API enable multi-criteria exploration (dataset, radius, and EC number), visualization, and data export in multiple formats. Sequence annotations from UniProt were refreshed and summarized as a normalized sequence-support score for ranking. Together, these updates establish RetroRules as a cross-domain resource bridging biochemistry and organic chemistry, offering broader coverage, controllable specificity, and enhanced usability for high-throughput pathway design, reaction prediction, and enzyme engineering.

Graphical Abstract