Cover Image

Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Sengar, Aditya, Hariri, Ali, Probst, Daniel, Barth, Patrick, Vandergheynst, Pierre
Format:	Preprint
Published:	2025
Subjects:	Biomolecules Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Beyond Ensembles: Simulating All-Atom Protein Dynamics in a Learned Latent Space
by: Sengar, Aditya, et al.
Published: (2025)

AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies
by: Martinkus, Karolis, et al.
Published: (2023)

Protein Conformation Generation via Force-Guided SE(3) Diffusion Models
by: Wang, Yan, et al.
Published: (2024)

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

Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure
by: Dunn, Ian, et al.
Published: (2023)

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

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

Towards More Accurate Full-Atom Antibody Co-Design
by: Wu, Jiayang, et al.
Published: (2025)

Modeling Dabrafenib Response Using Multi-Omics Modality Fusion and Protein Network Embeddings Based on Graph Convolutional Networks
by: Aman, La Ode, et al.
Published: (2025)

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

Function-Guided Conditional Generation Using Protein Language Models with Adapters
by: Yang, Jason, et al.
Published: (2024)

Diffusion Language Models Are Versatile Protein Learners
by: Wang, Xinyou, et al.
Published: (2024)

BadGraph: A Backdoor Attack Against Latent Diffusion Model for Text-Guided Graph Generation
by: Ye, Liang, et al.
Published: (2025)

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

ConforNets: Latents-Based Conformational Control in OpenFold3
by: Lee, Minji, et al.
Published: (2026)

Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space
by: Ketata, Mohamed Amine, et al.
Published: (2024)

MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
by: Wu, Lirong, et al.
Published: (2024)

Steering Generative Models with Experimental Data for Protein Fitness Optimization
by: Yang, Jason, et al.
Published: (2025)

DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding
by: Lin, Haitao, et al.
Published: (2022)

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space
by: Soldát, Matouš, et al.
Published: (2025)

PharMolixFM: All-Atom Foundation Models for Molecular Modeling and Generation
by: Luo, Yizhen, et al.
Published: (2025)

Graph Diffusion Transformers for Multi-Conditional Molecular Generation
by: Liu, Gang, et al.
Published: (2024)

Full-Atom Peptide Design with Geometric Latent Diffusion
by: Kong, Xiangzhe, et al.
Published: (2024)

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

Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering
by: Jiao, Shujian, et al.
Published: (2024)

Generative Model for Small Molecules with Latent Space RL Fine-Tuning to Protein Targets
by: Sob, Ulrich A. Mbou, et al.
Published: (2024)

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

GeoGraph: Geometric and Graph-based Ensemble Descriptors for Intrinsically Disordered Proteins
by: Quinn, Eoin, et al.
Published: (2025)

Multi-Objective Latent Space Optimization of Generative Molecular Design Models
by: Abeer, A N M Nafiz, et al.
Published: (2022)

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

TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation
by: Zongying, Lin, et al.
Published: (2024)

Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design
by: Klarner, Leo, et al.
Published: (2024)

Automated Neuron Labelling Enables Generative Steering and Interpretability in Protein Language Models
by: Banerjee, Arjun, et al.
Published: (2025)

STAR-GO: Improving Protein Function Prediction by Learning to Hierarchically Integrate Ontology-Informed Semantic Embeddings
by: Akça, Mehmet Efe, et al.
Published: (2025)

Open-Source Protein Language Models for Function Prediction and Protein Design
by: Pandi, Shivasankaran Vanaja, et al.
Published: (2024)

Steering Protein Language Models
by: Huang, Long-Kai, et al.
Published: (2025)

Molecular Diffusion Models with Virtual Receptors
by: Halfon, Matan, et al.
Published: (2024)

Rethinking Molecular Design: Integrating Latent Variable and Auto-Regressive Models for Goal Directed Generation
by: Arthur-Loui, Heath, et al.
Published: (2024)

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

Full-Atom Peptide Design based on Multi-modal Flow Matching
by: Li, Jiahan, et al.
Published: (2024)