Modeling protein-protein,protein-peptide,and protein-oligosaccharide complexes: CAPRI 7th edition

We present the seventh report on the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions. Performance was evaluated on the basis of 36 114 models of protein complexes submitted by 57 groups—including 13 automatic servers—in prediction rounds held during the years 2016 to 2019 for eight protein-protein, three protein-peptide, and five protein-oligosaccharide targets with different length ligands. Six of the protein-protein targets represented challenging hetero-complexes, due to factors such as availability of distantly related templates for the individual subunits, or for the full complex, inter-domain flexibility, conformational adjustments at the binding region, or the multi-component nature of the complex. The main challenge for the protein-peptide and protein-oligosaccharide complexes was to accurately model the ligand conformation and its interactions at the interface. Encouragingly, models of acceptable quality, or better, were obtained for a total of six protein-protein complexes, which included four of the challenging hetero-complexes and a homo-decamer. But fewer of these targets were predicted with medium or higher accuracy. High accuracy models were obtained for two of the three protein-peptide targets, and for one of the protein-oligosaccharide targets. The remaining protein-sugar targets were predicted with medium accuracy. Our analysis indicates that progress in predicting increasingly challenging and diverse types of targets is due to closer integration of template-based modeling techniques with docking, scoring, and model refinement procedures, and to significant incremental improvements in the underlying methodologies.