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FLOWR integrates continuous and categorical flow matching with equivariant optimal transport, enhanced by an efficient protein pocket conditioning. Alongside FLOWR, we present SPINDR, a curated dataset comprising ligand\u2013pocket cocrystal complexes specifically designed to address existing data quality issues. Empirical evaluations demonstrate that FLOWR surpasses current state-of-the-art diffusion- and flow-based methods in terms of PoseBusters-validity, pose accuracy and interaction recovery, while offering an inference speed-up, achieving up to 70-fold faster performance. In addition, we introduce FLOWR.MULTI, a highly accurate multi-purpose model allowing for the targeted sampling of ligands that adhere to predefined interaction profiles and chemical substructures for fragment-based design without the need of retraining or any resampling strategies. Collectively, our results indicate that FLOWR and FLOWR.MULTI represent an advancement in artificial intelligence-driven structure-based drug design, substantially enhancing the reliability and applicability of de novo, interaction- and fragment-based ligand generation in real-world drug discovery settings.<\/jats:p>","DOI":"10.1038\/s43588-026-00998-8","type":"journal-article","created":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T09:02:46Z","timestamp":1779958966000},"page":"565-574","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["FLOWR: flow matching for structure-aware de novo, interaction- and fragment-based ligand generation"],"prefix":"10.1038","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6319-7283","authenticated-orcid":false,"given":"Julian","family":"Cremer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0067-8313","authenticated-orcid":false,"given":"Ross","family":"Irwin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9070-740X","authenticated-orcid":false,"given":"Alessandro","family":"Tibo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7825-4797","authenticated-orcid":false,"given":"Jon Paul","family":"Janet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3927-7897","authenticated-orcid":false,"given":"Simon","family":"Olsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4191-2156","authenticated-orcid":false,"given":"Djork-Arn\u00e9","family":"Clevert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,28]]},"reference":[{"key":"998_CR1","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/j.chembiol.2003.09.002","volume":"10","author":"AC Anderson","year":"2003","unstructured":"Anderson, A. 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