A Model-Centric Review of Deep Learning for Protein Design
Fuente:
arXiv
Saved in:
| Main Authors: | Kyro, Gregory W., Qiu, Tianyin, Batista, Victor S. |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation
by: Kyro, Gregory W., et al.
Published: (2023)
by: Kyro, Gregory W., et al.
Published: (2023)
CardioGenAI: A Machine Learning-Based Framework for Re-Engineering Drugs for Reduced hERG Liability
by: Kyro, Gregory W., et al.
Published: (2024)
by: Kyro, Gregory W., et al.
Published: (2024)
Deep Learning for Protein Complex Prediction and Design
by: Xie, Ziwei
Published: (2026)
by: Xie, Ziwei
Published: (2026)
ContactNet: Geometric-Based Deep Learning Model for Predicting Protein-Protein Interactions
by: Halfon, Matan, et al.
Published: (2024)
by: Halfon, Matan, et al.
Published: (2024)
Deep Manifold Transformation for Protein Representation Learning
by: Hu, Bozhen, et al.
Published: (2024)
by: Hu, Bozhen, et al.
Published: (2024)
Open-Source Protein Language Models for Function Prediction and Protein Design
by: Pandi, Shivasankaran Vanaja, et al.
Published: (2024)
by: Pandi, Shivasankaran Vanaja, et al.
Published: (2024)
ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design
by: Ma, Yiming, et al.
Published: (2024)
by: Ma, Yiming, et al.
Published: (2024)
Advanced Deep Learning Methods for Protein Structure Prediction and Design
by: Zhang, Yichao, et al.
Published: (2025)
by: Zhang, Yichao, et al.
Published: (2025)
Accelerating Protein Molecular Dynamics Simulation with DeepJump
by: Costa, Allan dos Santos, et al.
Published: (2025)
by: Costa, Allan dos Santos, et al.
Published: (2025)
Importance Weighted Expectation-Maximization for Protein Sequence Design
by: Song, Zhenqiao, et al.
Published: (2023)
by: Song, Zhenqiao, et al.
Published: (2023)
Reinforcement Learning for Sequence Design Leveraging Protein Language Models
by: Subramanian, Jithendaraa, et al.
Published: (2024)
by: Subramanian, Jithendaraa, et al.
Published: (2024)
SurfPro: Functional Protein Design Based on Continuous Surface
by: Song, Zhenqiao, et al.
Published: (2024)
by: Song, Zhenqiao, et al.
Published: (2024)
Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design
by: Klarner, Leo, et al.
Published: (2024)
by: Klarner, Leo, et al.
Published: (2024)
A Comprehensive Review of Emerging Approaches in Machine Learning for De Novo PROTAC Design
by: Gharbi, Yossra, et al.
Published: (2024)
by: Gharbi, Yossra, et al.
Published: (2024)
Steering Protein Language Models
by: Huang, Long-Kai, et al.
Published: (2025)
by: Huang, Long-Kai, et al.
Published: (2025)
Hierarchical Multi-Label Contrastive Learning for Protein-Protein Interaction Prediction Across Organisms
by: Liu, Shiyi, et al.
Published: (2025)
by: Liu, Shiyi, et al.
Published: (2025)
Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization
by: Qiu, Jiahao, et al.
Published: (2024)
by: Qiu, Jiahao, et al.
Published: (2024)
Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design
by: Tagasovska, Nataša, et al.
Published: (2024)
by: Tagasovska, Nataša, et al.
Published: (2024)
Protein Inverse Folding From Structure Feedback
by: Xu, Junde, et al.
Published: (2025)
by: Xu, Junde, et al.
Published: (2025)
Structure-Informed Protein Language Model
by: Zhang, Zuobai, et al.
Published: (2024)
by: Zhang, Zuobai, et al.
Published: (2024)
Exploiting Hierarchical Interactions for Protein Surface Learning
by: Lin, Yiqun, et al.
Published: (2024)
by: Lin, Yiqun, 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)
by: Shah, Aayush, 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)
Protein Design with Dynamic Protein Vocabulary
by: Liu, Nuowei, et al.
Published: (2025)
by: Liu, Nuowei, et al.
Published: (2025)
Protein Structure Prediction in the 3D HP Model Using Deep Reinforcement Learning
by: Espitia, Giovanny, et al.
Published: (2024)
by: Espitia, Giovanny, et al.
Published: (2024)
Cross-Chirality Generalization by Axial Vectors for Hetero-Chiral Protein-Peptide Interaction Design
by: Yang, Ziyi, et al.
Published: (2026)
by: Yang, Ziyi, et al.
Published: (2026)
Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2
by: Lin, Yeqing, et al.
Published: (2024)
by: Lin, Yeqing, et al.
Published: (2024)
Machine Learning Coarse-Grained Potentials of Protein Thermodynamics
by: Majewski, Maciej, et al.
Published: (2022)
by: Majewski, Maciej, et al.
Published: (2022)
Multi-Scale Representation Learning for Protein Fitness Prediction
by: Zhang, Zuobai, et al.
Published: (2024)
by: Zhang, Zuobai, et al.
Published: (2024)
AtomSurf : Surface Representation for Learning on Protein Structures
by: Mallet, Vincent, et al.
Published: (2023)
by: Mallet, Vincent, et al.
Published: (2023)
Peptide Sequencing Via Protein Language Models
by: Pham, Thuong Le Hoai, et al.
Published: (2024)
by: Pham, Thuong Le Hoai, et al.
Published: (2024)
Structure Language Models for Protein Conformation Generation
by: Lu, Jiarui, et al.
Published: (2024)
by: Lu, Jiarui, et al.
Published: (2024)
Diffusion Language Models Are Versatile Protein Learners
by: Wang, Xinyou, et al.
Published: (2024)
by: Wang, Xinyou, et al.
Published: (2024)
Learning Structure, Energy, and Dynamics: A Survey of Artificial Intelligence for Protein Dynamics
by: Tang, Haocheng, et al.
Published: (2026)
by: Tang, Haocheng, et al.
Published: (2026)
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
by: Zhou, Xiangxin, et al.
Published: (2025)
by: Zhou, Xiangxin, et al.
Published: (2025)
Advances in Protein Representation Learning: Methods, Applications, and Future Directions
by: Nguyen, Viet Thanh Duy, et al.
Published: (2025)
by: Nguyen, Viet Thanh Duy, et al.
Published: (2025)
A Geometric Graph-Based Deep Learning Model for Drug-Target Affinity Prediction
by: Rana, Md Masud, et al.
Published: (2025)
by: Rana, Md Masud, et al.
Published: (2025)
Interpreting and Steering Protein Language Models through Sparse Autoencoders
by: Garcia, Edith Natalia Villegas, et al.
Published: (2025)
by: Garcia, Edith Natalia Villegas, et al.
Published: (2025)
Steering Generative Models with Experimental Data for Protein Fitness Optimization
by: Yang, Jason, et al.
Published: (2025)
by: Yang, Jason, et al.
Published: (2025)
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters
by: Arts, Marloes, et al.
Published: (2023)
by: Arts, Marloes, et al.
Published: (2023)
Similar Items
-
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation
by: Kyro, Gregory W., et al.
Published: (2023) -
CardioGenAI: A Machine Learning-Based Framework for Re-Engineering Drugs for Reduced hERG Liability
by: Kyro, Gregory W., et al.
Published: (2024) -
Deep Learning for Protein Complex Prediction and Design
by: Xie, Ziwei
Published: (2026) -
ContactNet: Geometric-Based Deep Learning Model for Predicting Protein-Protein Interactions
by: Halfon, Matan, et al.
Published: (2024) -
Deep Manifold Transformation for Protein Representation Learning
by: Hu, Bozhen, et al.
Published: (2024)