Fig. 2: Accuracy of CombFold on Benchmark 1.

a, The top-N (N = 1, 5, 10) success rate of CombFold (blue) and AFM (orange). AFM produces only five predictions. b, Predicted confidence versus the TM-score for CombFold. c, Success rate of AFM in producing pairwise interactions as measured by the pairwise connectivity versus the TM-score of the models produced by CombFold. d, TM-score of AFM models versus CombFold models. e, eIF2B:eIF2 complex: CombFold model (left) and cryo-EM structure (right). The model contains over 1,500 additional amino acids (marked with red circles). f, GID E3 ubiquitin ligase complex: high-quality CombFold model (left), cryo-EM structure (middle) and inaccurate AFM model (right). g, Multiple resistance and pH adaptation (Mrp) complex: inaccurate CombFold model (left), cryo-EM structure (middle) and high-quality AFM model (right). h, Human mitochondrial translocase TIM22: high-quality model by CombFold, integrating experimental crosslinking data (left), cryo-EM structure (middle) and inaccurate AFM model (right). Crosslinks are shown as blue lines.