How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver

Accurate chemical structure resolution from textual identifiers such as names and CAS RN® is critical for computational modeling in chemistry and related fields. This paper introduces MoleculeResolver, an automated, robust Python-based tool designed to address inconsistencies and inaccuracies commonly encountered when converting chemical identifiers to canonical SMILES strings. MoleculeResolver systematically crosschecks structures retrieved from multiple reputable chemical databases, implements rigorous identifier plausibility checks, standardizes molecular structures, and intelligently selects the most accurate representation based on a unique resolution algorithm. SCIENTIFIC CONTRIBUTION: Benchmarks across diverse datasets confirm that MoleculeResolver significantly enhances precision, recall, and overall reliability compared to traditional single-source methods, proving its utility as a valuable resource for chemists, data scientists, and researchers engaged in high-quality molecular data analysis and predictive model development.

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Publication Details

Journal
Journal of Cheminformatics
Published
2025-08-04
DOI
https://doi.org/10.1186/s13321-025-01064-7
Citations
3
Primary Topic
Computational Drug Discovery Methods
Type
article
Field-Weighted Citation Impact
4.51
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article

How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver

S. Müller
3 citations
Journal of Cheminformatics
Computational Drug Discovery Methods
4.51
article

How to crack a SMILES: automatic crosschecked chemical structure resolution across multiple services using MoleculeResolver

S. Müller
article en
3 citations

Abstract

Accurate chemical structure resolution from textual identifiers such as names and CAS RN® is critical for computational modeling in chemistry and related fields. This paper introduces MoleculeResolver, an automated, robust Python-based tool designed to address inconsistencies and inaccuracies commonly encountered when converting chemical identifiers to canonical SMILES strings. MoleculeResolver systematically crosschecks structures retrieved from multiple reputable chemical databases, implements rigorous identifier plausibility checks, standardizes molecular structures, and intelligently selects the most accurate representation based on a unique resolution algorithm. SCIENTIFIC CONTRIBUTION: Benchmarks across diverse datasets confirm that MoleculeResolver significantly enhances precision, recall, and overall reliability compared to traditional single-source methods, proving its utility as a valuable resource for chemists, data scientists, and researchers engaged in high-quality molecular data analysis and predictive model development.

Journal of CheminformaticsVol. 17(1)
Universität Hamburg (DE), Hamburg University of Technology (DE)
Industry, innovation and infrastructure
Openalex Percentile: Top 5%
Computational Drug Discovery Methods
4.51
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