{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Pacesa M"],"funding":["Swiss National Science Foundation","European Research Council","NIH HHS","NIGMS NIH HHS"],"pagination":["483-492"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12507698"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["646(8084)"],"pubmed_abstract":["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. <sup>1</sup>) 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 the"],"journal":["Nature"],"pubmed_title":["One-shot design of functional protein binders with BindCraft."],"pmcid":["PMC12507698"],"funding_grant_id":["R35 GM138368","214936","DP5 OD026389","948783"],"pubmed_authors":["Yachnin BJ","Goverde CA","Schwank G","Choudhury J","Gonczy P","Lindhoud S","Schellhaas C","Ghamary KH","Schmidt J","Vecchio AJ","Swarts DC","Buckley S","Nickel L","Georgeon S","Hatzopoulos GN","Pacesa M","Cho Y","Ovchinnikov S","Westphal AH","Schneider BL","Kapoor S","Wollacott AM","Correia BE","Barendse P","Kissling L","Pyatova E","Alcaraz-Serna A","Muller YD","Vinue L"],"additional_accession":[]},"is_claimable":false,"name":"One-shot design of functional protein binders with BindCraft.","description":"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. <sup>1</sup>) 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 the","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Oct","modification":"2026-06-04T09:20:14.441Z","creation":"2026-05-07T03:12:52.784Z"},"accession":"S-EPMC12507698","cross_references":{"pubmed":["40866699"],"doi":["10.1038/s41586-025-09429-6"]}}