Cover Image

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

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Tang, Haocheng, Shi, Liang, Zhang, Ya-Shi, Liu, Xixian, Tang, Jian, Lu, Jiarui
Format:	Preprint
Published:	2026
Subjects:	Biomolecules Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics
by: Shi, Liang, et al.
Published: (2026)

Structure Language Models for Protein Conformation Generation
by: Lu, Jiarui, et al.
Published: (2024)

Structure-Informed Protein Language Model
by: Zhang, Zuobai, et al.
Published: (2024)

Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
by: Lu, Jiarui, et al.
Published: (2024)

Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling
by: Lu, Jiarui, et al.
Published: (2023)

ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation
by: Zhang, Zuobai, et al.
Published: (2024)

Aligning Protein Conformation Ensemble Generation with Physical Feedback
by: Lu, Jiarui, et al.
Published: (2025)

Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
by: Zhou, Xiangxin, et al.
Published: (2025)

Multi-Scale Representation Learning for Protein Fitness Prediction
by: Zhang, Zuobai, et al.
Published: (2024)

Protein Design with Dynamic Protein Vocabulary
by: Liu, Nuowei, et al.
Published: (2025)

Hierarchical Multi-Label Contrastive Learning for Protein-Protein Interaction Prediction Across Organisms
by: Liu, Shiyi, et al.
Published: (2025)

Accelerating Protein Molecular Dynamics Simulation with DeepJump
by: Costa, Allan dos Santos, et al.
Published: (2025)

SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction
by: Huang, Yanwen, et al.
Published: (2024)

Exploiting Hierarchical Interactions for Protein Surface Learning
by: Lin, Yiqun, et al.
Published: (2024)

AtomSurf : Surface Representation for Learning on Protein Structures
by: Mallet, Vincent, et al.
Published: (2023)

Docking-Aware Attention: Dynamic Protein Representations through Molecular Context Integration
by: Sicherman, Amitay, et al.
Published: (2025)

Auxiliary Discrminator Sequence Generative Adversarial Networks (ADSeqGAN) for Few Sample Molecule Generation
by: Tang, Haocheng, et al.
Published: (2025)

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming
by: Xu, Minkai, et al.
Published: (2021)

HemePLM-Diffuse: A Scalable Generative Framework for Protein-Ligand Dynamics in Large Biomolecular System
by: Thakur, Rakesh, et al.
Published: (2025)

MoDyGAN: Combining Molecular Dynamics With GANs to Investigate Protein Conformational Space
by: Liang, Jingbo, et al.
Published: (2025)

Learning Protein Structure-Function Relationships through Knowledge-guided Representation Decomposition
by: Wang, Mingqing, et al.
Published: (2026)

A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation
by: Tang, Xiangru, et al.
Published: (2024)

Protein Inverse Folding From Structure Feedback
by: Xu, Junde, et al.
Published: (2025)

Advanced Deep Learning Methods for Protein Structure Prediction and Design
by: Zhang, Yichao, et al.
Published: (2025)

Compact Artificial Neural Network Models for Predicting Protein Residue -- RNA Base Binding
by: Selitskiy, Stanislav
Published: (2025)

DISPROTBENCH: Uncovering the Functional Limits of Protein Structure Prediction Models in Intrinsically Disordered Regions
by: Zeng, Xinyue, et al.
Published: (2025)

Energy Efficient Protein Language Models: Leveraging Small Language Models with LoRA for Controllable Protein Generation
by: Shah, Aayush, et al.
Published: (2024)

A Protein Structure Prediction Approach Leveraging Transformer and CNN Integration
by: Zhou, Yanlin, et al.
Published: (2024)

Orientation-Aware Graph Neural Networks for Protein Structure Representation Learning
by: Li, Jiahan, et al.
Published: (2022)

Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2
by: Lin, Yeqing, et al.
Published: (2024)

Proteomic Learning of Gamma-Aminobutyric Acid (GABA) Receptor-Mediated Anesthesia
by: Jiang, Jian, et al.
Published: (2025)

MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training
by: Chen, Bo, et al.
Published: (2024)

ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings
by: Hanke, Josef, et al.
Published: (2026)

Conformation-Aware Structure Prediction of Antigen-Recognizing Immune Proteins
by: Dreyer, Frédéric A., et al.
Published: (2025)

Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters
by: Arts, Marloes, et al.
Published: (2023)

Training Dynamics of Learning 3D-Rotational Equivariance
by: Shen, Max W., et al.
Published: (2025)

ContactNet: Geometric-Based Deep Learning Model for Predicting Protein-Protein Interactions
by: Halfon, Matan, et al.
Published: (2024)

Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship
by: Ko, Eunji, et al.
Published: (2024)

A Model-Centric Review of Deep Learning for Protein Design
by: Kyro, Gregory W., et al.
Published: (2025)

Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction
by: Yu, Ziyang, et al.
Published: (2024)