VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification
Fuente:
arXiv
Saved in:
| Main Authors: | Sestak, Florian, Schneckenreiter, Lisa, Brandstetter, Johannes, Hochreiter, Sepp, Mayr, Andreas, Klambauer, Günter |
|---|---|
| Format: | Preprint |
| Published: |
2024
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences
by: Schmidinger, Niklas, et al.
Published: (2024)
by: Schmidinger, Niklas, et al.
Published: (2024)
GNN-VPA: A Variance-Preserving Aggregation Strategy for Graph Neural Networks
by: Schneckenreiter, Lisa, et al.
Published: (2024)
by: Schneckenreiter, Lisa, et al.
Published: (2024)
EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction
by: Zhang, Yang, et al.
Published: (2023)
by: Zhang, Yang, et al.
Published: (2023)
LaM-SLidE: Latent Space Modeling of Spatial Dynamical Systems via Linked Entities
by: Sestak, Florian, et al.
Published: (2025)
by: Sestak, Florian, et al.
Published: (2025)
Design of Ligand-Binding Proteins with Atomic Flow Matching
by: Liu, Junqi, et al.
Published: (2024)
by: Liu, Junqi, et al.
Published: (2024)
An Energy-Adaptive Elastic Equivariant Transformer Framework for Protein Structure Representation
by: Zhang, Zhongyue, et al.
Published: (2025)
by: Zhang, Zhongyue, et al.
Published: (2025)
Beyond Olfaction: New Insights into Human Odorant Binding Proteins
by: Chen, Mifen, et al.
Published: (2025)
by: Chen, Mifen, et al.
Published: (2025)
PLD-Tree: Persistent Laplacian Decision Tree for Protein-Protein Binding Free Energy Prediction
by: Xu, Xingjian, et al.
Published: (2024)
by: Xu, Xingjian, et al.
Published: (2024)
Flow-Based Fragment Identification via Binding Site-Specific Latent Representations
by: Neeser, Rebecca Manuela, et al.
Published: (2025)
by: Neeser, Rebecca Manuela, et al.
Published: (2025)
PETIMOT: A Novel Framework for Inferring Protein Motions from Sparse Data Using SE(3)-Equivariant Graph Neural Networks
by: Lombard, Valentin, et al.
Published: (2025)
by: Lombard, Valentin, et al.
Published: (2025)
Compact Artificial Neural Network Models for Predicting Protein Residue -- RNA Base Binding
by: Selitskiy, Stanislav
Published: (2025)
by: Selitskiy, Stanislav
Published: (2025)
Hermes: Large DEL Datasets Train Generalizable Protein-Ligand Binding Prediction Models
by: Kleinsasser, Maxwell, et al.
Published: (2026)
by: Kleinsasser, Maxwell, et al.
Published: (2026)
Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction
by: Yu, Ziyang, et al.
Published: (2024)
by: Yu, Ziyang, et al.
Published: (2024)
DecoyDB: A Dataset for Graph Contrastive Learning in Protein-Ligand Binding Affinity Prediction
by: Zhang, Yupu, et al.
Published: (2025)
by: Zhang, Yupu, et al.
Published: (2025)
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
by: Lin, Haitao, et al.
Published: (2024)
by: Lin, Haitao, et al.
Published: (2024)
Persistent Directed Flag Laplacian (PDFL)-Based Machine Learning for Protein-Ligand Binding Affinity Prediction
by: Zia, Mushal, et al.
Published: (2024)
by: Zia, Mushal, et al.
Published: (2024)
Exploring Data-Driven Chemical SMILES Tokenization Approaches to Identify Key Protein-Ligand Binding Moieties
by: Temizer, Asu Büşra, et al.
Published: (2022)
by: Temizer, Asu Büşra, et al.
Published: (2022)
Mimicking the Gas-Phase to Transport Odorants through the Nasal Mucus: Functional Insights into Odorant Binding Proteins
by: Paesani, Massimiliano, et al.
Published: (2024)
by: Paesani, Massimiliano, et al.
Published: (2024)
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation
by: Kantroo, Pranav, et al.
Published: (2024)
by: Kantroo, Pranav, et al.
Published: (2024)
ETDock: A Novel Equivariant Transformer for Protein-Ligand Docking
by: Yi, Yiqiang, et al.
Published: (2023)
by: Yi, Yiqiang, et al.
Published: (2023)
ViDTA: Enhanced Drug-Target Affinity Prediction via Virtual Graph Nodes and Attention-based Feature Fusion
by: Li, Minghui, et al.
Published: (2024)
by: Li, Minghui, et al.
Published: (2024)
Hybrid Quantum Neural Networks for Efficient Protein-Ligand Binding Affinity Prediction
by: Jeong, Seon-Geun, et al.
Published: (2025)
by: Jeong, Seon-Geun, et al.
Published: (2025)
Site4Drug: Predicting Drug-Binding Target Sites with an AI Agent
by: Kim, Taehan, et al.
Published: (2026)
by: Kim, Taehan, et al.
Published: (2026)
Diffusion Sequence Models for Enhanced Protein Representation and Generation
by: Hallee, Logan, et al.
Published: (2025)
by: Hallee, Logan, et al.
Published: (2025)
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding
by: Lin, Haitao, et al.
Published: (2022)
by: Lin, Haitao, et al.
Published: (2022)
Multiview Random Vector Functional Link Network for Predicting DNA-Binding Proteins
by: Quadir, A., et al.
Published: (2024)
by: Quadir, A., et al.
Published: (2024)
ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings
by: Hanke, Josef, et al.
Published: (2026)
by: Hanke, Josef, et al.
Published: (2026)
FABind: Fast and Accurate Protein-Ligand Binding
by: Pei, Qizhi, et al.
Published: (2023)
by: Pei, Qizhi, et al.
Published: (2023)
Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering
by: Jiao, Shujian, et al.
Published: (2024)
by: Jiao, Shujian, et al.
Published: (2024)
Score-Based Generative Models for Designing Binding Peptide Backbones
by: Boom, John D, et al.
Published: (2023)
by: Boom, John D, et al.
Published: (2023)
Protein FID: Improved Evaluation of Protein Structure Generative Models
by: Faltings, Felix, et al.
Published: (2025)
by: Faltings, Felix, et al.
Published: (2025)
CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction
by: Han, Rong, et al.
Published: (2024)
by: Han, Rong, et al.
Published: (2024)
Fold-switching Proteins
by: Chakravarty, Devlina, et al.
Published: (2025)
by: Chakravarty, Devlina, et al.
Published: (2025)
Remodeling Peptide-MHC-TCR Triad Binding as Sequence Fusion for Immunogenicity Prediction
by: Ma, Jiahao, et al.
Published: (2025)
by: Ma, Jiahao, et al.
Published: (2025)
SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation
by: Xue, Fanglei, et al.
Published: (2025)
by: Xue, Fanglei, et al.
Published: (2025)
GeoGraph: Geometric and Graph-based Ensemble Descriptors for Intrinsically Disordered Proteins
by: Quinn, Eoin, et al.
Published: (2025)
by: Quinn, Eoin, et al.
Published: (2025)
Orientation-Aware Graph Neural Networks for Protein Structure Representation Learning
by: Li, Jiahan, et al.
Published: (2022)
by: Li, Jiahan, et al.
Published: (2022)
Decoding How Proteins Fold
by: Vila, Jorge
Published: (2025)
by: Vila, Jorge
Published: (2025)
Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding with LLMs
by: Wu, Wei, et al.
Published: (2024)
by: Wu, Wei, et al.
Published: (2024)
EquiJump: Protein Dynamics Simulation via SO(3)-Equivariant Stochastic Interpolants
by: Costa, Allan dos Santos, et al.
Published: (2024)
by: Costa, Allan dos Santos, et al.
Published: (2024)
Similar Items
-
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences
by: Schmidinger, Niklas, et al.
Published: (2024) -
GNN-VPA: A Variance-Preserving Aggregation Strategy for Graph Neural Networks
by: Schneckenreiter, Lisa, et al.
Published: (2024) -
EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction
by: Zhang, Yang, et al.
Published: (2023) -
LaM-SLidE: Latent Space Modeling of Spatial Dynamical Systems via Linked Entities
by: Sestak, Florian, et al.
Published: (2025) -
Design of Ligand-Binding Proteins with Atomic Flow Matching
by: Liu, Junqi, et al.
Published: (2024)