{"entity": "publication", "iuid": "85647eabbe644ebf93336f6e2534b98b", "timestamp": "2026-08-20T20:57:51.378Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/85647eabbe644ebf93336f6e2534b98b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/85647eabbe644ebf93336f6e2534b98b"}}, "title": "Peptide binder design with inverse folding and protein structure prediction.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2023-10-25", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "6", "issue": "1", "pages": "229", "issn-l": null}, "abstract": "The computational design of peptide binders towards a specific protein interface can aid diagnostic and therapeutic efforts. Here, we design peptide binders by combining the known structural space searched with Foldseek, the protein design method ESM-IF1, and AlphaFold2 (AF) in a joint framework. Foldseek generates backbone seeds for a modified version of ESM-IF1 adapted to protein complexes. The resulting sequences are evaluated with AF using an MSA representation for the receptor structure and a single sequence for the binder. We show that AF can accurately evaluate protein binders and that our bind score can select these (ROC AUC = 0.96 for the heterodimeric case). We find that designs created from seeds with more contacts per residue are more successful and tend to be short. There is a relationship between the sequence recovery in interface positions and the plDDT of the designs, where designs with \u226580% recovery have an average plDDT of 84 compared to 55 at 0%. Designed sequences have 60% higher median plDDT values towards intended receptors than non-intended ones. Successful binders (predicted interface RMSD \u2264 2 \u00c5) are designed towards 185 (6.5%) heteromeric and 42 (3.6%) homomeric protein interfaces with ESM-IF1 compared with 18 (1.5%) using ProteinMPNN from 100 samples.", "doi": "10.1038/s42004-023-01029-7", "pmid": "37880344", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10600234"}, {"db": "pii", "key": "10.1038/s42004-023-01029-7"}], "notes": [], "created": "2026-08-20T09:25:36.744Z", "modified": "2026-08-20T09:25:36.805Z"}