ENSEMBITS: an alphabet of protein conformational ensembles
Fuente:
arXiv
Saved in:
| Main Authors: | Shi, Kaiwen, Oliver, Carlos |
|---|---|
| Format: | Preprint |
| Published: |
2026
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
A standard transformer and attention with linear biases for molecular conformer generation
by: Gurev, Viatcheslav, et al.
Published: (2025)
by: Gurev, Viatcheslav, et al.
Published: (2025)
BioBlobs: Unsupervised Discovery of Functional Substructures for Protein Function Prediction
by: Wang, Xin, et al.
Published: (2025)
by: Wang, Xin, et al.
Published: (2025)
Diffusion on language model encodings for protein sequence generation
by: Meshchaninov, Viacheslav, et al.
Published: (2024)
by: Meshchaninov, Viacheslav, et al.
Published: (2024)
Transformers trained on proteins can learn to attend to Euclidean distance
by: Ellmen, Isaac, et al.
Published: (2025)
by: Ellmen, Isaac, et al.
Published: (2025)
FoldToken2: Learning compact, invariant and generative protein structure language
by: Gao, Zhangyang, et al.
Published: (2024)
by: Gao, Zhangyang, et al.
Published: (2024)
PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural models
by: Neupane, Pawan, et al.
Published: (2025)
by: Neupane, Pawan, et al.
Published: (2025)
Zero-shot protein stability prediction by inverse folding models: a free energy interpretation
by: Frellsen, Jes, et al.
Published: (2025)
by: Frellsen, Jes, et al.
Published: (2025)
Learning conformational ensembles of proteins based on backbone geometry
by: Wolf, Nicolas, et al.
Published: (2025)
by: Wolf, Nicolas, et al.
Published: (2025)
Reaction Prediction via Interaction Modeling of Symmetric Difference Shingle Sets
by: Shi, Runhan, et al.
Published: (2025)
by: Shi, Runhan, et al.
Published: (2025)
PROflow: An iterative refinement model for PROTAC-induced structure prediction
by: Qiang, Bo, et al.
Published: (2024)
by: Qiang, Bo, et al.
Published: (2024)
RTMol: Rethinking Molecule-text Alignment in a Round-trip View
by: Chen, Letian, et al.
Published: (2025)
by: Chen, Letian, et al.
Published: (2025)
RNA Secondary Structure Prediction Using Transformer-Based Deep Learning Models
by: Zhou, Yanlin, et al.
Published: (2024)
by: Zhou, Yanlin, et al.
Published: (2024)
REBIND: Enhancing ground-state molecular conformation via force-based graph rewiring
by: Kim, Taewon, et al.
Published: (2024)
by: Kim, Taewon, et al.
Published: (2024)
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)
Representation choice shapes the interpretation of protein conformational dynamics
by: Giottonini, Axel, et al.
Published: (2026)
by: Giottonini, Axel, et al.
Published: (2026)
Inference-time optimization for experiment-grounded protein ensemble generation
by: Maddipatla, Advaith, et al.
Published: (2026)
by: Maddipatla, Advaith, et al.
Published: (2026)
Retrieval and competition: how a protein foundation model starts a protein
by: Jedryszek, Piotr, et al.
Published: (2026)
by: Jedryszek, Piotr, et al.
Published: (2026)
GENEOnet: A new machine learning paradigm based on Group Equivariant Non-Expansive Operators. An application to protein pocket detection
by: Bocchi, Giovanni, et al.
Published: (2022)
by: Bocchi, Giovanni, et al.
Published: (2022)
EnzyPGM: Pocket-conditioned Generative Model for Substrate-specific Enzyme Design
by: Lin, Zefeng, et al.
Published: (2026)
by: Lin, Zefeng, et al.
Published: (2026)
Deciphering Scientific Reasoning Steps from Outcome Data for Molecule Optimization
by: Liu, Zequn, et al.
Published: (2026)
by: Liu, Zequn, et al.
Published: (2026)
PCEvo: Path-Consistent Molecular Representation via Virtual Evolutionary
by: Li, Kun, et al.
Published: (2026)
by: Li, Kun, et al.
Published: (2026)
SEISMO: Increasing Sample Efficiency in Molecular Optimization with a Trajectory-Aware LLM Agent
by: Krüger, Fabian P., et al.
Published: (2026)
by: Krüger, Fabian P., et al.
Published: (2026)
Co-folding model guided by structural proteomics
by: Shtrikman, Alon, et al.
Published: (2026)
by: Shtrikman, Alon, et al.
Published: (2026)
Multimodal Alignment and Preference Optimization for Zero-Shot Conditional RNA Generation
by: Klypa, Roman, et al.
Published: (2026)
by: Klypa, Roman, et al.
Published: (2026)
PI-Mamba: Linear-Time Protein Backbone Generation via Spectrally Initialized Flow Matching
by: Wu, Tianyu, et al.
Published: (2026)
by: Wu, Tianyu, et al.
Published: (2026)
Structural Interpretations of Protein Language Model Representations via Differentiable Graph Partitioning
by: Dutta, Siddhant, et al.
Published: (2026)
by: Dutta, Siddhant, et al.
Published: (2026)
Tensor-DTI: Enhancing Biomolecular Interaction Prediction with Contrastive Embedding Learning
by: Gil-Sorribes, Manel, et al.
Published: (2026)
by: Gil-Sorribes, Manel, et al.
Published: (2026)
Drug Release Modeling using Physics-Informed Neural Networks
by: Qureshi, Daanish Aleem, et al.
Published: (2026)
by: Qureshi, Daanish Aleem, et al.
Published: (2026)
A Systematic Evaluation of Co-folding Model Representations for Small-Molecule Learning
by: Jang, Hyosoon, et al.
Published: (2026)
by: Jang, Hyosoon, et al.
Published: (2026)
BioLM-Score: Language-Prior Conditioned Probabilistic Geometric Potentials for Protein-Ligand Scoring
by: Yang, Zhangfan, et al.
Published: (2026)
by: Yang, Zhangfan, et al.
Published: (2026)
RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design
by: Kshirsagar, Meghana, et al.
Published: (2026)
by: Kshirsagar, Meghana, et al.
Published: (2026)
Bolek: A Multimodal Language Model for Molecular Reasoning
by: Grabowski, Frederic, et al.
Published: (2026)
by: Grabowski, Frederic, et al.
Published: (2026)
Prot2Chat: Protein LLM with Early-Fusion of Text, Sequence and Structure
by: Wang, Zhicong, et al.
Published: (2025)
by: Wang, Zhicong, et al.
Published: (2025)
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules
by: Feng, Shikun, et al.
Published: (2024)
by: Feng, Shikun, et al.
Published: (2024)
MODA: A Unified 3D Diffusion Framework for Multi-Task Target-Aware Molecular Generation
by: Xu, Dong, et al.
Published: (2025)
by: Xu, Dong, et al.
Published: (2025)
Auxiliary Discrminator Sequence Generative Adversarial Networks (ADSeqGAN) for Few Sample Molecule Generation
by: Tang, Haocheng, et al.
Published: (2025)
by: Tang, Haocheng, et al.
Published: (2025)
Do Protein Transformers Have Biological Intelligence?
by: Lin, Fudong, et al.
Published: (2025)
by: Lin, Fudong, et al.
Published: (2025)
Protein Design with Dynamic Protein Vocabulary
by: Liu, Nuowei, et al.
Published: (2025)
by: Liu, Nuowei, et al.
Published: (2025)
A Foundation Chemical Language Model for Comprehensive Fragment-Based Drug Discovery
by: Ho, Alexander, et al.
Published: (2025)
by: Ho, Alexander, et al.
Published: (2025)
Conditional Latent Space Molecular Scaffold Optimization for Accelerated Molecular Design
by: Boyar, Onur, et al.
Published: (2024)
by: Boyar, Onur, et al.
Published: (2024)
Similar Items
-
A standard transformer and attention with linear biases for molecular conformer generation
by: Gurev, Viatcheslav, et al.
Published: (2025) -
BioBlobs: Unsupervised Discovery of Functional Substructures for Protein Function Prediction
by: Wang, Xin, et al.
Published: (2025) -
Diffusion on language model encodings for protein sequence generation
by: Meshchaninov, Viacheslav, et al.
Published: (2024) -
Transformers trained on proteins can learn to attend to Euclidean distance
by: Ellmen, Isaac, et al.
Published: (2025) -
FoldToken2: Learning compact, invariant and generative protein structure language
by: Gao, Zhangyang, et al.
Published: (2024)