# DynaPPI: A Large-scale Dynamic Protein Dataset for AI-driven Advances in Protein Interactomics

arXiv: https://arxiv.org/abs/2608.10435 · HTML: https://mlsanity.com/paper/2608.10435/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 1 of its 32 references that are in the map.
- First posted on arXiv 11 Aug 2026.

## Builds on (most cited first, 1 of 1)

- [Dynamic PDB: A New Dataset and a SE(3) Model Extension by Integrating Dynamic Behaviors and Physical Properties in Protein Structures](https://mlsanity.com/paper/2408.12413/) (2024)

## Abstract (arXiv)

Diffusion models have been widely explored in protein backbone generation due to their powerful generation capabilities.However, in today's AI-driven biological research, predicting the structure of unknown multi-chain protein aggregates (called "complexes" in biology) remains an unsolved challenge.This is because existing static or dynamic protein datasets focus solely on static snapshots or single-entity trajectories, neglecting the dynamic process of multiple monomers forming complexes.To alleviate this dilemma, we present DynaPPI, a dynamic protein dataset comprising molecular dynamics (MD) trajectories of protein complex formation from dissociated chains to the bound state, as a pivotal resource to bridge the gap between static structural biology and the inherently temporal nature of dynamic molecular interactions.Benefiting from this dataset, diffusion models can explicitly learn the dynamic binding trajectories of known complexes and accurately predict the structures of unknown complexes based on their diverse generative properties, thereby further catalyzing AI-driven structural biology and protein interactomics.