Cover Image

PETIMOT: A Novel Framework for Inferring Protein Motions from Sparse Data Using SE(3)-Equivariant Graph Neural Networks

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Lombard, Valentin, Grudinin, Sergei, Laine, Elodie
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

BAnG: Bidirectional Anchored Generation for Conditional RNA Design
by: Klypa, Roman, et al.
Published: (2025)

Multimodal Alignment and Preference Optimization for Zero-Shot Conditional RNA Generation
by: Klypa, Roman, et al.
Published: (2026)

ETDock: A Novel Equivariant Transformer for Protein-Ligand Docking
by: Yi, Yiqiang, et al.
Published: (2023)

SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation
by: Xue, Fanglei, et al.
Published: (2025)

EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction
by: Zhang, Yang, et al.
Published: (2023)

VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification
by: Sestak, Florian, et al.
Published: (2024)

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

Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation
by: Huguet, Guillaume, et al.
Published: (2024)

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

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)

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

Interpreting and Steering Protein Language Models through Sparse Autoencoders
by: Garcia, Edith Natalia Villegas, et al.
Published: (2025)

E3STO: Orbital Inspired SE(3)-Equivariant Molecular Representation for Electron Density Prediction
by: Mitnikov, Ilan, et al.
Published: (2024)

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

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

Graph Neural Networks in Modern AI-aided Drug Discovery
by: Zhang, Odin, et al.
Published: (2025)

EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants
by: Costa, Allan dos Santos, et al.
Published: (2024)

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

Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning
by: Kong, Xiangzhe, et al.
Published: (2023)

Ligandformer: A Graph Neural Network for Predicting Compound Property with Robust Interpretation
by: Guo, Jinjiang, et al.
Published: (2022)

A Review on Fragment-based De Novo 2D Molecule Generation
by: Voloboev, Sergei
Published: (2024)

De novo antibody design with SE(3) diffusion
by: Cutting, Daniel, et al.
Published: (2024)

GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking
by: Yuan, Yiliang, et al.
Published: (2024)

Symphony: Symmetry-Equivariant Point-Centered Spherical Harmonics for 3D Molecule Generation
by: Daigavane, Ameya, et al.
Published: (2023)

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

Structure-based Drug Design with Equivariant Diffusion Models
by: Schneuing, Arne, et al.
Published: (2022)

Investigating Graph Neural Networks and Classical Feature-Extraction Techniques in Activity-Cliff and Molecular Property Prediction
by: Dablander, Markus
Published: (2024)

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

3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information
by: Kuang, Taojie, et al.
Published: (2023)

Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings
by: Sengar, Aditya, et al.
Published: (2025)

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

Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms
by: Jing, Bowen, et al.
Published: (2023)

DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction
by: Zhang, Yupu, et al.
Published: (2025)

Towards Interpretable Protein Structure Prediction with Sparse Autoencoders
by: Parsan, Nithin, et al.
Published: (2025)

ProxelGen: Generating Proteins as 3D Densities
by: Faltings, Felix, et al.
Published: (2025)

Multiview Random Vector Functional Link Network for Predicting DNA-Binding Proteins
by: Quadir, A., et al.
Published: (2024)

Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers
by: Wang, Yingheng, et al.
Published: (2024)

RiboGen: RNA Sequence and Structure Co-Generation with Equivariant MultiFlow
by: Rubin, Dana, et al.
Published: (2025)

Hybrid Quantum Neural Networks for Efficient Protein-Ligand Binding Affinity Prediction
by: Jeong, Seon-Geun, et al.
Published: (2025)

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