# Learning Structure, Energy, and Dynamics: A Survey of Artificial Intelligence for Protein Dynamics

arXiv: https://arxiv.org/abs/2604.25244 · HTML: https://mlsanity.com/paper/2604.25244/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 68 of its 152 references that are in the map.
- First posted on arXiv 28 Apr 2026.

## Builds on (most cited first, 30 of 68)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Density estimation using Real NVP](https://mlsanity.com/paper/1605.08803/) (2016)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentials](https://mlsanity.com/paper/2202.02541/) (2022)
- [Equivariant flow matching](https://mlsanity.com/paper/2306.15030/) (2023)
- [Flow Annealed Importance Sampling Bootstrap](https://mlsanity.com/paper/2208.01893/) (2022)
- [Iterated Denoising Energy Matching for Sampling from Boltzmann Densities](https://mlsanity.com/paper/2402.06121/) (2024)
- [AlphaFold Meets Flow Matching for Generating Protein Ensembles](https://mlsanity.com/paper/2402.04845/) (2024)
- [Normalizing Flows are Capable Generative Models](https://mlsanity.com/paper/2412.06329/) (2024)
- [SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials](https://mlsanity.com/paper/2209.10702/) (2022)
- [Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics](https://mlsanity.com/paper/2302.00600/) (2023)
- [Machine Learning of coarse-grained Molecular Dynamics Force Fields](https://mlsanity.com/paper/1812.01736/) (2018)
- [Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics](https://mlsanity.com/paper/2302.01170/) (2023)
- [Coarse Graining Molecular Dynamics with Graph Neural Networks](https://mlsanity.com/paper/2007.11412/) (2020)
- [Smooth Normalizing Flows](https://mlsanity.com/paper/2110.00351/) (2021)
- [Generative Modeling of Molecular Dynamics Trajectories](https://mlsanity.com/paper/2409.17808/) (2024)
- [Transferable Boltzmann Generators](https://mlsanity.com/paper/2406.14426/) (2024)
- [Protein Conformation Generation via Force-Guided SE(3) Diffusion Models](https://mlsanity.com/paper/2403.14088/) (2024)
- [Scalable Equilibrium Sampling with Sequential Boltzmann Generators](https://mlsanity.com/paper/2502.18462/) (2025)
- [Machine Learning Coarse-Grained Potentials of Protein Thermodynamics](https://mlsanity.com/paper/2212.07492/) (2022)
- [Flow-matching -- efficient coarse-graining of molecular dynamics without forces](https://mlsanity.com/paper/2203.11167/) (2022)
- [Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling](https://mlsanity.com/paper/2306.03117/) (2023)
- [Progressive Inference-Time Annealing of Diffusion Models for Sampling from Boltzmann Densities](https://mlsanity.com/paper/2506.16471/) (2025)
- [Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration](https://mlsanity.com/paper/1801.00203/) (2017)
- [Navigating protein landscapes with a machine-learned transferable coarse-grained model](https://mlsanity.com/paper/2310.18278/) (2023)
- [Consistent Sampling and Simulation: Molecular Dynamics with Energy-Based Diffusion Models](https://mlsanity.com/paper/2506.17139/) (2025)
- [Structure Language Models for Protein Conformation Generation](https://mlsanity.com/paper/2410.18403/) (2024)
- [EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants](https://mlsanity.com/paper/2410.09667/) (2024)
- [SimpleFold: Folding Proteins is Simpler than You Think](https://mlsanity.com/paper/2509.18480/) (2025)
- [DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations for Protein Folding](https://mlsanity.com/paper/1909.07817/) (2019)

## Built on by (most cited first, 1 of 1)

- [Bi-FORK: Generative Modeling of High-Dimensional Bifurcating Systems](https://mlsanity.com/paper/2610.12449/) (2026)

## Abstract (arXiv)

Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances in artificial intelligence for protein dynamics from three perspectives: learning from structural ensembles and trajectories, learning from physical energy signals, and learning to accelerate molecular simulations. We summarize representative methods for conformation ensemble generation, trajectory generation, Boltzmann generators, physics-aware adaptation, machine learning potentials, coarse-grained modeling, and collective variable discovery. We further discuss available datasets and key open challenges, such as scalability, thermodynamic consistency, kinetic fidelity, and integration with experimental constraints.