DynaPIN: A Tool for Characterizing Dynamic Protein Interfaces

Static structural models often fail to capture the dynamic mechanisms of protein interactions. To address this, we introduce DynaPIN, an open-source pipeline for extracting dynamic interface fingerprints from molecular simulations of protein complexes. Our tool unifies quality control, interface accuracy assessment, and atomistic interaction analyses into a single automated workflow, accessible at https://github.com/CSB-KaracaLab/DynaPIN. A key feature of the pipeline is its dynamic interface definition that classifies residues based on the persistence of their interface status over the simulation. Applying DynaPIN to varying docking difficulty (rigid, medium, and difficult) targets from the DynaBench dataset reveals that interface flexibility diverges from traditional docking difficulty classifications. Furthermore, we show that DynaPIN's dynamic descriptors can directly be linked to each complex's biological role. Ultimately, by delivering standardized, frame-resolved outputs, DynaPIN facilitates mechanistic insights into protein interactions and provides datasets to train future dynamics-aware artificial intelligence models.