Fig. 8: Analysis of a large dataset of 923 complexes from the Eukaryotic Linear Motif (ELM) database.

a Distribution of the 923 ELM cases that could be modeled and evaluated among 84 ELM categories (ELM types), highlighting the unbalanced distribution, biased towards some receptor/ligand couples such as the LIG_LIR_Gen_1, LIG_Actin_CPI_1 and LIG_Rb_LxCxE_1 categories comprising 132, 62 and 40 cases, respectively. Dark gray bars indicate the cases with an exact reference PDB structure while light gray bars indicate the cases that could be evaluated using a homologous PDB structure (see Methods). b Histogram representing the success rates obtained with six different protocols applied to the dataset extracted from the ELM database. The average success rates are reported with same color codes as in Figs. 2 and 5 but using white hatched bars (full-length ligand delimitation (deep purple), with extension of 100 amino acids (purple), with no alignment (cyan), mixed or unpaired co-alignments (blue), and combined (green)). The average success rates were calculated from a repeated stratified sampling of 1000 iterations over the 84 ELM categories, randomly selecting one ELM complex in each of the 84 categories. At every iteration, success rates were calculated and the mean success rate value is reported in the histogram where the best AlphaFold2 (AF2)-Multimer model (best AF2 confidence score) is of Acceptable (light color), Medium (medium color) or High (dark color) quality according to the CAPRI criteria for protein-peptide complexes⁴⁹. Source data are provided as a Source Data file.