Work

Representing chemical and enzymatic reactions in fingerprint space for applicability filtering and classification

Year: 2026

Type: article

Abstract: Molecular and reaction fingerprints are widely used as static descriptors, but their relationship to graph-level reaction application remains unclear. We address this question in counted Extended-Connectivity Fingerprint (ECFP) space, representing reactions as signed differences between product and substrate fingerprints. We define ECFP-compatible templates, for which graph-level reaction application induces a constant fingerprint displacement, yielding a functorial mapping from graph transformations to affine translations in fingerprint space. We also introduce reaction-center ECFPs to encode the local environments required for template application and to provide a fast coordinate-wise prefilter for graph-level reaction applicability. We evaluate this framework on USPTO-50k and MetaNetX reactions across a range of ECFP radii. Both representations carry predictive information for reaction-class and enzyme-class classification, with reaction-center ECFPs contributing information not captured by reaction ECFPs alone. This framework connects reaction templates and reaction fingerprints to molecular pathway search and reaction-property prediction in fingerprint space.

Source: Journal of Cheminformatics

DOI: 10.1186/s13321-026-01322-2

Authors: Philippe Meyer, Thomas Duigou, Guillaume Gricourt, Jean-Loup Faulon

Institutions: AgroParisTech, Université Paris-Saclay, Microbiologie de l’alimentation au service de la santé, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Language: English

Topic: Computational Drug Discovery Methods

Subfield: Drug Discovery

Field: Pharmacology, Toxicology and Pharmaceutics

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,390

Funder: Agence Nationale de la Recherche