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Here, we present Scaffold Generator, a comprehensive open library for the generation, handling, and display of molecular scaffolds, scaffold trees and networks. The new library is based on the Chemistry Development Kit (CDK) and highly customisable through multiple settings, e.g. five different structural framework definitions are available. For display of scaffold hierarchies, the open GraphStream Java library is utilised. Performance snapshots with natural products (NP) from the COCONUT (COlleCtion of Open Natural prodUcTs) database and drug molecules from DrugBank are reported. The generation of a scaffold network from more than 450,000 NP can be achieved within a single day.<\/jats:p>","DOI":"10.1186\/s13321-022-00656-x","type":"journal-article","created":{"date-parts":[[2022,11,10]],"date-time":"2022-11-10T10:04:38Z","timestamp":1668074678000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK)"],"prefix":"10.1186","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1554-6666","authenticated-orcid":false,"given":"Jonas","family":"Schaub","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8197-076X","authenticated-orcid":false,"given":"Julian","family":"Zander","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0722-4229","authenticated-orcid":false,"given":"Achim","family":"Zielesny","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6966-0814","authenticated-orcid":false,"given":"Christoph","family":"Steinbeck","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,11,10]]},"reference":[{"issue":"19","key":"656_CR1","doi-asserted-by":"publisher","first-page":"2894","DOI":"10.1002\/(SICI)1521-3773(19991004)38:19<2894::AID-ANIE2894>3.0.CO;2-F","volume":"38","author":"G Schneider","year":"1999","unstructured":"Schneider G, Neidhart W, Giller T, Schmid G (1999) \u201cScaffold-Hopping\u201d by topological pharmacophore search: a contribution to virtual screening. 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