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Here, we present <jats:italic>Cheminformatics Microservice V3<\/jats:italic>, a significant update to the existing platform that provides unified programmatic access to cheminformatics libraries, including RDKit, Chemistry Development Kit (CDK), and Open Babel through a RESTful API framework. This latest version features a newly developed, interactive web-based frontend built with React, providing users with an intuitive graphical interface for manipulating and analysing chemical structures. The frontend supports essential cheminformatics operations, including structure editing, PubChem database integration, batch molecular processing, and standardised InChI\/RInChI identifier generation. The microservice V3 addresses critical accessibility barriers in computational chemistry by providing researchers with immediate access to analytical tools, eliminating the need for specialised technical expertise or complex software installations. This approach facilitates reproducible research workflows and broadens the utilisation of cheminformatics methodologies across interdisciplinary research communities. The platform is publicly accessible at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/app.naturalproducts.net\" ext-link-type=\"uri\">https:\/\/app.naturalproducts.net<\/jats:ext-link>, and the complete source code and documentation are available on GitHub.<\/jats:p>","DOI":"10.1186\/s13321-025-01094-1","type":"journal-article","created":{"date-parts":[[2025,9,23]],"date-time":"2025-09-23T09:45:25Z","timestamp":1758620725000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Cheminformatics Microservice V3: a web portal for chemical structure manipulation and analysis"],"prefix":"10.1186","volume":"17","author":[{"given":"Kohulan","family":"Rajan","sequence":"first","affiliation":[]},{"given":"Venkata","family":"Chandrasekhar","sequence":"additional","affiliation":[]},{"given":"Nisha","family":"Sharma","sequence":"additional","affiliation":[]},{"given":"Sri Ram Sagar","family":"Kanakam","sequence":"additional","affiliation":[]},{"given":"Felix","family":"Baensch","sequence":"additional","affiliation":[]},{"given":"Christoph","family":"Steinbeck","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,9,23]]},"reference":[{"key":"1094_CR1","volume-title":"Methods in pharmacology and toxicology; methods in pharmacology and toxicology","author":"P Ambure","year":"2014","unstructured":"Ambure P, Aher RB, Roy K (2014) Recent advances in the open access cheminformatics toolkits, software tools, workflow environments, and databases. 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