Fig. 2: Score vs. RMSD to the crystal structure for 10,000 docked models generated for each complex in the benchmark set using AlphaFold2 models as docking input. | Nature Communications

Fig. 2: Score vs. RMSD to the crystal structure for 10,000 docked models generated for each complex in the benchmark set using AlphaFold2 models as docking input.

From: Protein complex prediction using Rosetta, AlphaFold, and mass spectrometry covalent labeling

Fig. 2: Score vs. RMSD to the crystal structure for 10,000 docked models generated for each complex in the benchmark set using AlphaFold2 models as docking input.The alternative text for this image may have been generated using AI.

The top-scoring models are marked by a black star and aligned to the crystal structure. Actin/gs1 is shown in green, β−2-microglobulin in blue, and insulin structures in pink. The RMSD of the top-scoring model is indicated next to the marked point. a RosettaDock Isc versus RMSD (without CL data). b Covalent labeling score versus RMSD (with CL data). Covalent labeling scores are less negative than Isc scores due to the addition of positive penalty scores. c Top-scoring complex model predictions using covalent labeling score aligned to the native crystal structures (dark gray). d Top-ranked models generated by AlphaFold-Multimer aligned to native crystal structure. RMSDs are listed for each complex. Source data are provided as a Source Data file.

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