Fig. 1: AF3 performance in predicting LaP structures.

A AF3 predictions on known LaP structures, with experimentally determined structures display in each group, RMSD were calculated on Cα atoms. The structure ribbon is colored from blue at the N-terminus to red at the C-terminus. Isopeptide ^isoC—^isoN distances were measured between the N atom of the N-terminus residue and the C atom of the carboxyl group in the isopeptide donor residues (Asp or Glu in the 7^th/8^th/9^th position). The dashed frames indicate the classification color pattern used in panel (B). B Pie chart showing the performance of AF3 on PDB-deposited LaPs, with predicted structures classified into three categories. A predicted structure is classified as having a “lasso fold” if the wrapping is observed with a C–N bond distance of less than 4.0 Å. C AF3 predictions for 12 LaPs with a known plug position but not deposited in the PDB. D Pie chart showing the performance of AF3 on LaPs with known plug position but not deposited PDB structures, with predicted structures classified into three categories, using the same color pattern as in panel (A). E AF3 predictions for LaPs with unknown structures. The illustrated LaPs were randomly selected from the RODEO dataset, employing stratified sampling based on total sequence length. A more comprehensive test involving 40 randomly-selected lasso peptide sequences is shown in Table S3. Lasso scores refer to the potential of peptide sequences to be classified as lasso peptides, predicted from RODEO. The sequences for the representative LaPs are available in Table S4. F Pie chart showing the structure prediction results corresponding to Table S3, with predicted structures classified into two categories (lasso shape and non-lasso shape), as the true plug positions are unknown.