AF-M predictions accompanying the manuscript: Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions

The set of all AlphaFold multimer (AF-M) v2.3 pairwise structure predictions accompanying the publication: Predictomes: A classifier-curated database of AlphaFold-modeled protein-protein interactions. This dataset includes prediction pairs used for training random forest classifiers including SPOC, pairs used for 30 ranking experiments, all pairs that belong to the genome maintenance matrix on predictomes.org, and three proteome wide in-silico interaction screens conducted with human DONSON, human STK19, and human USP37. All pairs were generated with ColabFold v1.5.2. All our predictions used AF-M multimer version 3 weights models 1, 2, and 4 with 3 recycles, templates enabled, 1 ensemble, no dropout, and no AMBER relaxation. The Multiple Sequence Alignments (MSAs) (unpaired + paired) supplied to AF-M were generated by the MMSeqs2 server using default settings. Sequences run were generally capped at 3,600 amino acids total to avoid memory exhaustion on GPUs.