Chemical Structures Cleaning Center: An Open Web Service for Automated Chemical Databases Curation
- 1DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry
- 2Universidad Nacional Autónoma de México
Abstract
Chemical database curation is an essential step in chemoinformatics workflows. Omitting this process or using inadequate curation protocols adversely affects structure-dependent computational methods that rely on high-quality data, such as quantitative structure–activity relationship models, physicochemical property prediction, and molecular similarity calculations. Although database curation is compulsory as machine learning, chemoinformatics, and computational chemistry in general rely on data quality, existing public databases curation pipelines are predominantly developed in coding environments like Python and hosted on different servers. While efficient, these tools often present a steep learning curve for researchers without programming expertise or domain specialists seeking to integrate chemoinformatics into their projects. To bridge this gap, herein we present Chemical Structures Cleaning Center, an automated, user-friendly, and open-access web application designed for streamlining chemical database curation. The tool builds upon well-validated and used protocols to curate chemical libraries. To illustrate the platform's utility, we used a small chemical database containing reference compounds to test various pipeline tasks, such as counterion desalting, duplicate detection, small-molecule salt handling, preservation of complex stereochemical integrity, and reduction of metal-organic salts. The curation pipeline provides references to relevant manuscripts highlighting the importance of chemical database curation. The web page is freely available at https://huggingface.co/spaces/Dannmarquez16/Chemical-Structures-Cleaning-Center
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BibTeX
@misc{ramirezmarquez2026chemical,
title = {{Chemical Structures Cleaning Center: An Open Web Service for Automated Chemical Databases Curation}},
author = {Carlos D. Ramírez-Márquez and José L. Medina-Franco},
howpublished = {ChemRxiv},
year = {2026},
month = sep,
doi = {10.26434/chemrxiv.15009294/v1},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009294/v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Chemical Structures Cleaning Center: An Open Web Service for Automated Chemical Databases Curation
AU - Carlos D. Ramírez-Márquez
AU - José L. Medina-Franco
PY - 2026
DA - 2026/09/22
PB - ChemRxiv
DO - 10.26434/chemrxiv.15009294/v1
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009294/v1
AB - Chemical database curation is an essential step in chemoinformatics workflows. Omitting this process or using inadequate curation protocols adversely affects structure-dependent computational methods that rely on high-quality data, such as quantitative structure–activity relationship models, physicochemical property prediction, and molecular similarity calculations. Although database curation is compulsory as machine learning, chemoinformatics, and computational chemistry in general rely on data quality, existing public databases curation pipelines are predominantly developed in coding environments like Python and hosted on different servers. While efficient, these tools often present a steep learning curve for researchers without programming expertise or domain specialists seeking to integrate chemoinformatics into their projects. To bridge this gap, herein we present Chemical Structures Cleaning Center, an automated, user-friendly, and open-access web application designed for streamlining chemical database curation. The tool builds upon well-validated and used protocols to curate chemical libraries. To illustrate the platform's utility, we used a small chemical database containing reference compounds to test various pipeline tasks, such as counterion desalting, duplicate detection, small-molecule salt handling, preservation of complex stereochemical integrity, and reduction of metal-organic salts. The curation pipeline provides references to relevant manuscripts highlighting the importance of chemical database curation. The web page is freely available at https://huggingface.co/spaces/Dannmarquez16/Chemical-Structures-Cleaning-Center
ER -