{"title":"KNIME Workflows for Chemoinformatic Characterization of Chemical Databases.","authors":"Carlos D Ramírez-Márquez, José L Medina-Franco","doi":"10.1002/minf.202400337","DOIUrl":null,"url":null,"abstract":"<p><p>In chemoinformatics, chemical databases have great importance since their main objective is to store and organize the chemical structures of molecules and their properties, from basic information such as chemical structure to more complex like molecular fingerprints or other types of calculated or experimental descriptors and biological activity. However, this data can only be utilized in projects to identify novel therapeutic molecules or other fields through their correct characterization and analysis. In this Application Note, we compiled five workflows within the open-source data analytics and visualization platform KNIME that can be implemented for the chemoinformatic characterization of databases. To illustrate the application of the workflows, we used BIOFACQUIM, a compound database of natural products isolated and characterized in Mexico [1].</p>","PeriodicalId":18853,"journal":{"name":"Molecular Informatics","volume":"44 2","pages":"e202400337"},"PeriodicalIF":2.8000,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Informatics","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1002/minf.202400337","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
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Abstract
In chemoinformatics, chemical databases have great importance since their main objective is to store and organize the chemical structures of molecules and their properties, from basic information such as chemical structure to more complex like molecular fingerprints or other types of calculated or experimental descriptors and biological activity. However, this data can only be utilized in projects to identify novel therapeutic molecules or other fields through their correct characterization and analysis. In this Application Note, we compiled five workflows within the open-source data analytics and visualization platform KNIME that can be implemented for the chemoinformatic characterization of databases. To illustrate the application of the workflows, we used BIOFACQUIM, a compound database of natural products isolated and characterized in Mexico [1].
期刊介绍：
Molecular Informatics is a peer-reviewed, international forum for publication of high-quality, interdisciplinary research on all molecular aspects of bio/cheminformatics and computer-assisted molecular design. Molecular Informatics succeeded QSAR & Combinatorial Science in 2010.
Molecular Informatics presents methodological innovations that will lead to a deeper understanding of ligand-receptor interactions, macromolecular complexes, molecular networks, design concepts and processes that demonstrate how ideas and design concepts lead to molecules with a desired structure or function, preferably including experimental validation.
The journal''s scope includes but is not limited to the fields of drug discovery and chemical biology, protein and nucleic acid engineering and design, the design of nanomolecular structures, strategies for modeling of macromolecular assemblies, molecular networks and systems, pharmaco- and chemogenomics, computer-assisted screening strategies, as well as novel technologies for the de novo design of biologically active molecules. As a unique feature Molecular Informatics publishes so-called "Methods Corner" review-type articles which feature important technological concepts and advances within the scope of the journal.
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