Fig. 3: Assessing ternary complex formation. | Nature Communications

Fig. 3: Assessing ternary complex formation.

From: Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry

Fig. 3: Assessing ternary complex formation.The alternative text for this image may have been generated using AI.

a The minimum I-RMSD over time during the WE-HDX simulations of the PROTAC 2 system. Each green line indicates one replica (n = 7) and the black line is the average between all runs. The blue line indicates the minimum I-RMSD for a vanilla molecular dynamics simulation. b A scatter plot of the free energy vs the minimum I-RMSD of each of the 500 clusters from the PROTAC 2 simulations. The circles are colored by w-RMSD. c The predicted binding rates for the PROTAC 1 system (purple) and the ACBI1 system (green). The black line is the experimental binding rate determined via SPR. Source data are provided as a Source Data file.

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