Unlocking hidden biomolecular conformational landscapes in diffusion models at inference time
Fuente:
arXiv
Saved in:
| Main Authors: | Richman, Daniel D., Karaguesian, Jessica, Suomivuori, Carl-Mikael, Dror, Ron O. |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Integrative modelling of biomolecular dynamics
by: Gusew, Daria, et al.
Published: (2025)
by: Gusew, Daria, et al.
Published: (2025)
ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
by: Viswanath, Siddharth, et al.
Published: (2024)
by: Viswanath, Siddharth, 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)
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
by: Didi, Kieran, et al.
Published: (2023)
by: Didi, Kieran, et al.
Published: (2023)
De novo antibody design with SE(3) diffusion
by: Cutting, Daniel, et al.
Published: (2024)
by: Cutting, Daniel, et al.
Published: (2024)
On diffusion posterior sampling via sequential Monte Carlo for zero-shot scaffolding of protein motifs
by: Young, James Matthew, et al.
Published: (2024)
by: Young, James Matthew, et al.
Published: (2024)
RapidDock: Unlocking Proteome-scale Molecular Docking
by: Powalski, Rafał, et al.
Published: (2024)
by: Powalski, Rafał, et al.
Published: (2024)
Physics-informed generative model for drug-like molecule conformers
by: Williams, David C., et al.
Published: (2024)
by: Williams, David C., et al.
Published: (2024)
Classifier-free graph diffusion for molecular property targeting
by: Ninniri, Matteo, et al.
Published: (2023)
by: Ninniri, Matteo, et al.
Published: (2023)
Pharmacophore-guided de novo drug design with diffusion bridge
by: Wang, Conghao, et al.
Published: (2024)
by: Wang, Conghao, et al.
Published: (2024)
Mask prior-guided denoising diffusion improves inverse protein folding
by: Bai, Peizhen, et al.
Published: (2024)
by: Bai, Peizhen, et al.
Published: (2024)
ENSEMBITS: an alphabet of protein conformational ensembles
by: Shi, Kaiwen, et al.
Published: (2026)
by: Shi, Kaiwen, et al.
Published: (2026)
E(3)-invariant diffusion model for pocket-aware peptide generation
by: Liang, Po-Yu, et al.
Published: (2024)
by: Liang, Po-Yu, et al.
Published: (2024)
Personalised Medicine: Establishing predictive machine learning models for drug responses in patient derived cell culture
by: Abdel-Rehim, Abbi, et al.
Published: (2024)
by: Abdel-Rehim, Abbi, et al.
Published: (2024)
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)
ActivityDiff: A diffusion model with Positive and Negative Activity Guidance for De Novo Drug Design
by: Zhou, Renyi, et al.
Published: (2025)
by: Zhou, Renyi, et al.
Published: (2025)
A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization
by: Qiao, Anjie, et al.
Published: (2025)
by: Qiao, Anjie, et al.
Published: (2025)
Inference-time optimization for experiment-grounded protein ensemble generation
by: Maddipatla, Advaith, et al.
Published: (2026)
by: Maddipatla, Advaith, et al.
Published: (2026)
Large scale paired antibody language models
by: Kenlay, Henry, et al.
Published: (2024)
by: Kenlay, Henry, et al.
Published: (2024)
The need to implement FAIR principles in biomolecular simulations
by: Amaro, Rommie, et al.
Published: (2024)
by: Amaro, Rommie, et al.
Published: (2024)
Few-shot Protein Fitness Prediction via In-context Learning and Test-time Training
by: Teufel, Felix, et al.
Published: (2025)
by: Teufel, Felix, et al.
Published: (2025)
Higher-Order Message Passing for Glycan Representation Learning
by: Joeres, Roman, et al.
Published: (2024)
by: Joeres, Roman, et al.
Published: (2024)
ProteinGuide: On-the-fly property guidance for protein sequence generative models
by: Xiong, Junhao, et al.
Published: (2025)
by: Xiong, Junhao, et al.
Published: (2025)
Score-based 3D molecule generation with neural fields
by: Kirchmeyer, Matthieu, et al.
Published: (2025)
by: Kirchmeyer, Matthieu, et al.
Published: (2025)
Token-Mol 1.0: Tokenized drug design with large language model
by: Wang, Jike, et al.
Published: (2024)
by: Wang, Jike, et al.
Published: (2024)
Machine learning and natural language processing models to predict the extent of food processing
by: Arora, Nalin, et al.
Published: (2024)
by: Arora, Nalin, et al.
Published: (2024)
Matching biomolecular structures by registration of point clouds
by: Habeck, Michael, et al.
Published: (2024)
by: Habeck, Michael, et al.
Published: (2024)
RNACG: A Universal RNA Sequence Conditional Generation model based on Flow-Matching
by: Gao, Letian, et al.
Published: (2024)
by: Gao, Letian, et al.
Published: (2024)
Towards protein folding pathways by reconstructing protein residue networks with a policy-driven model
by: Khor, Susan
Published: (2026)
by: Khor, Susan
Published: (2026)
TerraBind: Fast and Accurate Binding Affinity Prediction through Coarse Structural Representations
by: Rossi, Matteo, et al.
Published: (2026)
by: Rossi, Matteo, et al.
Published: (2026)
Scalable Inference-Time Annealing with Surrogate Likelihood Estimators
by: Peñaherrera, Daniel, et al.
Published: (2026)
by: Peñaherrera, Daniel, et al.
Published: (2026)
A unified cross-attention model for predicting antigen binding specificity to both HLA and TCR molecules
by: Yu, Chenpeng, et al.
Published: (2024)
by: Yu, Chenpeng, et al.
Published: (2024)
Reinforcement-guided generative protein language models enable de novo design of highly diverse AAV capsids
by: Ferraz, Lucas, et al.
Published: (2026)
by: Ferraz, Lucas, et al.
Published: (2026)
BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery
by: John, Peter St., et al.
Published: (2024)
by: John, Peter St., et al.
Published: (2024)
Molecular Diffusion Models with Virtual Receptors
by: Halfon, Matan, et al.
Published: (2024)
by: Halfon, Matan, et al.
Published: (2024)
Pharmacophore-based design by learning on voxel grids
by: Mahmood, Omar, et al.
Published: (2025)
by: Mahmood, Omar, et al.
Published: (2025)
Structure-based drug design by denoising voxel grids
by: Pinheiro, Pedro O., et al.
Published: (2024)
by: Pinheiro, Pedro O., et al.
Published: (2024)
Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings
by: Sengar, Aditya, et al.
Published: (2025)
by: Sengar, Aditya, et al.
Published: (2025)
Rethinking Performance Measures of RNA Secondary Structure Problems
by: Runge, Frederic, et al.
Published: (2023)
by: Runge, Frederic, et al.
Published: (2023)
FLOWR.root: A flow matching based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction
by: Cremer, Julian, et al.
Published: (2025)
by: Cremer, Julian, et al.
Published: (2025)
Similar Items
-
Integrative modelling of biomolecular dynamics
by: Gusew, Daria, et al.
Published: (2025) -
ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
by: Viswanath, Siddharth, et al.
Published: (2024) -
Representation choice shapes the interpretation of protein conformational dynamics
by: Giottonini, Axel, et al.
Published: (2026) -
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
by: Didi, Kieran, et al.
Published: (2023) -
De novo antibody design with SE(3) diffusion
by: Cutting, Daniel, et al.
Published: (2024)