Fig. 1: General presentation of the benchmark dataset.

a Disentangling the complexity of a protein interaction network (sketched on the left) by analyzing binary interactions between a central gray protein and its blue binding partners can be complicated in case they contain intrinsically disordered regions. b General pipeline to select the PDB entries that can be used as test complexes from those released after May 2018. They were required to share no sequence or structural redundancy with any of the complex structures that were used for AlphaFold2-Multimer training. c Example illustrating filters used to assess the lack of redundancy between the candidate complex and structures published before May 2018. Two filters were used, one based on sequence identity using a 30% seq. id. threshold and a second retrieving all complexes involving a receptor homolog using PPI3D⁵⁷ and checking for lack of interface structural similarity using MM-align⁵⁹. d Boxplots showing the cumulative size distribution of the 42 inputs (receptor+ligand) that were processed by AlphaFold2, either in protocols where sequences were delineated following the boundaries of the experimental structures or in those where full lengths of ligands and/or receptors were used. In the boxplot representation center line is the median, min and max limits of the box are the lower and upper quartiles, whiskers are the 1.5x interquartile range and points represent outliers. Source data are provided as a Source Data file.