Structural Isomer Cumulative molecular fingerprinting method (SIC) for standardizing structural isomeric relationships
Year: 2025
Type: article
Abstract: Standardizing structural isomeric relationships and evaluating their distribution in chemical space remain major challenges in cheminformatics. Conventional molecular fingerprints and dimensionality reduction techniques are often sensitive to dataset size and structural complexity. Here, we introduce a molecular fingerprint, Structural Isomer Cumulative molecular fingerprint (SIC), that quantitatively captures relative structural differences among isomers with high precision. SIC consists of two variables: SICem, representing exact mass, and SICL, a cumulative descriptor derived from substructural differences. SICL enables calculation of relative structural distances within isomeric groups regardless of dataset size or molecular complexity. Using SIC, we successfully quantified structural differences across positional, skeletal, and functional group isomers, which were not adequately captured by existing descriptors. Furthermore, a scatter plot of SICem and SICL visualized metabolite distributions among cellular compartments, and nine endogenous metabolites were identified whose structural characteristics suggest potential toxicity. Standardizing structural isomeric relationships and evaluating their distribution in chemical space remain significant challenges in cheminformatics. Here, the authors propose a molecular fingerprinting method that can quantitatively capture structural differences within isomeric compound groups regardless of dataset size and despite increased molecular complexity.
Source: Communications Chemistry
Author: Taihei Torigoe
Language: English
Subfield: Computational Theory and Mathematics
Field: Computer Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $3,690
OpenAlex ID: W4417265257