DynaBench: Dynamic data for the docking benchmark

Protein-protein interactions are central to numerous cellular processes, including transport, signaling, and immune response. Structural modeling of protein assemblies typically relies on AlphaFold or docking methods, which produce structural models evaluated against a single experimental reference. While AlphaFold2 and its extension, AlphaFold-Multimer, have advanced complex prediction, they, and conventional docking tools, offer only static representations. However, flexibility at protein-protein interfaces is increasingly recognized as critical for function. To address this limitation, DynaBench provides a benchmark of interface dynamics in biologically relevant protein assemblies. We performed MD simulations for over 200 protein-protein complexes listed in the Docking Benchmark 5.5 (https://zlab.umassmed.edu/benchmark/), generating three 100 ns long replicas per complex. All trajectories are now publicly available online (http://www-lbt.ibpc.fr/DynaBench) via the MDposit platform (INRIA node), which is part of the EU-funded Molecular Dynamics Data Bank (MDDB). These simulations offer a unique resource for exploring interfacial flexibility, training machine learning models, redefining accuracy metrics for model evaluation, and informing the design of protein interfaces.