Figure 8
From: Predicting Protein–protein Association Rates using Coarse-grained Simulation and Machine Learning
(a) Flowchart of the overall prediction framework, in which multiple trajectories of the KMC simulation are used to calculate kon. In parallel, three indicators are calculated based on the structural and energetic features at the binding interface of the query protein complex. These indicators are input into a trained “complex decision tree” to identify potential overestimation, and then the kon calculated from the KMC simulations is adjusted based on the machine learning output. (b) Procedures involved in the KMC simulation. The detailed simulation algorithm is described in the Methods.
