biostudies-literaturePacesa MSwiss National Science FoundationEuropean Research CouncilNIH HHSNIGMS NIH HHS483-492https://www.ebi.ac.uk/biostudies/studies/S-EPMC12507698biostudies-literatureUnknown646(8084)Protein-protein interactions are at the core of all key biological processes. However, the complexity of the structural features that determine protein-protein interactions makes their design challenging. Here we present BindCraft, an open-source and automated pipeline for de novo protein binder design with experimental success rates of 10-100%. BindCraft leverages the weights of AlphaFold2 (ref. ¹) to generate binders with nanomolar affinity without the need for high-throughput screening or experimental optimization, even in the absence of known binding sites. We successfully designed binders against a diverse set of challenging targets, including cell-surface receptors, common allergens, de novo designed proteins and multi-domain nucleases, such as CRISPR-Cas9. We showcase theNatureOne-shot design of functional protein binders with BindCraft.PMC12507698R35 GM138368214936DP5 OD026389948783Yachnin BJGoverde CASchwank GChoudhury JGonczy PLindhoud SSchellhaas CGhamary KHSchmidt JVecchio AJSwarts DCBuckley SNickel LGeorgeon SHatzopoulos GNPacesa MCho YOvchinnikov SWestphal AHSchneider BLKapoor SWollacott AMCorreia BEBarendse PKissling LPyatova EAlcaraz-Serna AMuller YDVinue LfalseOne-shot design of functional protein binders with BindCraft.Protein-protein interactions are at the core of all key biological processes. However, the complexity of the structural features that determine protein-protein interactions makes their design challenging. Here we present BindCraft, an open-source and automated pipeline for de novo protein binder design with experimental success rates of 10-100%. BindCraft leverages the weights of AlphaFold2 (ref. ¹) to generate binders with nanomolar affinity without the need for high-throughput screening or experimental optimization, even in the absence of known binding sites. We successfully designed binders against a diverse set of challenging targets, including cell-surface receptors, common allergens, de novo designed proteins and multi-domain nucleases, such as CRISPR-Cas9. We showcase the2025-01-01T00:00:00Z2025 Oct2026-06-04T09:20:14.441Z2026-05-07T03:12:52.784ZS-EPMC125076984086669910.1038/s41586-025-09429-6