Protein Design with Dynamic Protein Vocabulary
Fuente:
arXiv
Saved in:
| Main Authors: | Liu, Nuowei, Kuang, Jiahao, Liu, Yanting, Ji, Tao, Sun, Changzhi, Lan, Man, Wu, Yuanbin |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
PDFBench: A Benchmark for De novo Protein Design from Function
by: Kuang, Jiahao, et al.
Published: (2025)
by: Kuang, Jiahao, et al.
Published: (2025)
EvoLlama: Enhancing LLMs' Understanding of Proteins via Multimodal Structure and Sequence Representations
by: Liu, Nuowei, et al.
Published: (2024)
by: Liu, Nuowei, et al.
Published: (2024)
Improving Protein Sequence Design through Designability Preference Optimization
by: Xue, Fanglei, et al.
Published: (2025)
by: Xue, Fanglei, et al.
Published: (2025)
Generative AI for Controllable Protein Sequence Design: A Survey
by: Zhu, Yiheng, et al.
Published: (2024)
by: Zhu, Yiheng, et al.
Published: (2024)
ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings
by: Kong, Zitai, et al.
Published: (2025)
by: Kong, Zitai, et al.
Published: (2025)
FABind: Fast and Accurate Protein-Ligand Binding
by: Pei, Qizhi, et al.
Published: (2023)
by: Pei, Qizhi, et al.
Published: (2023)
Monte Carlo Tree Diffusion with Multiple Experts for Protein Design
by: Liu, Xuefeng, et al.
Published: (2025)
by: Liu, Xuefeng, et al.
Published: (2025)
Advanced Deep Learning Methods for Protein Structure Prediction and Design
by: Zhang, Yichao, et al.
Published: (2025)
by: Zhang, Yichao, et al.
Published: (2025)
PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction
by: Wu, Lirong, et al.
Published: (2024)
by: Wu, Lirong, et al.
Published: (2024)
Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designer
by: Tan, Cheng, et al.
Published: (2023)
by: Tan, Cheng, et al.
Published: (2023)
Do Protein Transformers Have Biological Intelligence?
by: Lin, Fudong, et al.
Published: (2025)
by: Lin, Fudong, et al.
Published: (2025)
Constrained Diffusion for Protein Design with Hard Structural Constraints
by: Christopher, Jacob K., et al.
Published: (2025)
by: Christopher, Jacob K., et al.
Published: (2025)
Multi-level Interaction Modeling for Protein Mutational Effect Prediction
by: Mo, Yuanle, et al.
Published: (2024)
by: Mo, Yuanle, et al.
Published: (2024)
ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering
by: Shen, Yiqing, et al.
Published: (2024)
by: Shen, Yiqing, et al.
Published: (2024)
Reinforcement Learning for Sequence Design Leveraging Protein Language Models
by: Subramanian, Jithendaraa, et al.
Published: (2024)
by: Subramanian, Jithendaraa, et al.
Published: (2024)
PFMBench: Protein Foundation Model Benchmark
by: Gao, Zhangyang, et al.
Published: (2025)
by: Gao, Zhangyang, et al.
Published: (2025)
Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship
by: Ko, Eunji, et al.
Published: (2024)
by: Ko, Eunji, et al.
Published: (2024)
TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering
by: Shen, Yiqing, et al.
Published: (2024)
by: Shen, Yiqing, et al.
Published: (2024)
EMOCPD: Efficient Attention-based Models for Computational Protein Design Using Amino Acid Microenvironment
by: Ling, Xiaoqi, et al.
Published: (2024)
by: Ling, Xiaoqi, et al.
Published: (2024)
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)
Bridge-IF: Learning Inverse Protein Folding with Markov Bridges
by: Zhu, Yiheng, et al.
Published: (2024)
by: Zhu, Yiheng, et al.
Published: (2024)
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation
by: Tang, Xiangru, et al.
Published: (2024)
by: Tang, Xiangru, et al.
Published: (2024)
RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design
by: Kshirsagar, Meghana, et al.
Published: (2026)
by: Kshirsagar, Meghana, et al.
Published: (2026)
AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on Protein Tertiary Structure Prediction
by: Yuan, Zhongju, et al.
Published: (2023)
by: Yuan, Zhongju, et al.
Published: (2023)
ProtCLIP: Function-Informed Protein Multi-Modal Learning
by: Zhou, Hanjing, et al.
Published: (2024)
by: Zhou, Hanjing, et al.
Published: (2024)
PRING: Rethinking Protein-Protein Interaction Prediction from Pairs to Graphs
by: Zheng, Xinzhe, et al.
Published: (2025)
by: Zheng, Xinzhe, et al.
Published: (2025)
From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?
by: Cao, Hanqun, et al.
Published: (2025)
by: Cao, Hanqun, et al.
Published: (2025)
Protein as a Second Language for LLMs
by: Chen, Xinhui, et al.
Published: (2025)
by: Chen, Xinhui, et al.
Published: (2025)
pLDDT-Predictor: High-speed Protein Screening Using Transformer and ESM2
by: Chae, Joongwon, et al.
Published: (2024)
by: Chae, Joongwon, et al.
Published: (2024)
Pre-Training Protein Bi-level Representation Through Span Mask Strategy On 3D Protein Chains
by: Zhao, Jiale, et al.
Published: (2024)
by: Zhao, Jiale, et al.
Published: (2024)
Enhancing Protein Predictive Models via Proteins Data Augmentation: A Benchmark and New Directions
by: Sun, Rui, et al.
Published: (2024)
by: Sun, Rui, et al.
Published: (2024)
General Protein Pretraining or Domain-Specific Designs? Benchmarking Protein Modeling on Realistic Applications
by: Yan, Shuo, et al.
Published: (2025)
by: Yan, Shuo, et al.
Published: (2025)
FoldToken: Learning Protein Language via Vector Quantization and Beyond
by: Gao, Zhangyang, et al.
Published: (2024)
by: Gao, Zhangyang, et al.
Published: (2024)
CCPL: Cross-modal Contrastive Protein Learning
by: Zheng, Jiangbin, et al.
Published: (2023)
by: Zheng, Jiangbin, et al.
Published: (2023)
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)
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)
Generative Active Learning for the Search of Small-molecule Protein Binders
by: Korablyov, Maksym, et al.
Published: (2024)
by: Korablyov, Maksym, et al.
Published: (2024)
Towards Interpretable Protein Structure Prediction with Sparse Autoencoders
by: Parsan, Nithin, et al.
Published: (2025)
by: Parsan, Nithin, et al.
Published: (2025)
PLM-eXplain: Divide and Conquer the Protein Embedding Space
by: van Eck, Jan, et al.
Published: (2025)
by: van Eck, Jan, et al.
Published: (2025)
Graph-level Protein Representation Learning by Structure Knowledge Refinement
by: Wang, Ge, et al.
Published: (2024)
by: Wang, Ge, et al.
Published: (2024)
Similar Items
-
PDFBench: A Benchmark for De novo Protein Design from Function
by: Kuang, Jiahao, et al.
Published: (2025) -
EvoLlama: Enhancing LLMs' Understanding of Proteins via Multimodal Structure and Sequence Representations
by: Liu, Nuowei, et al.
Published: (2024) -
Improving Protein Sequence Design through Designability Preference Optimization
by: Xue, Fanglei, et al.
Published: (2025) -
Generative AI for Controllable Protein Sequence Design: A Survey
by: Zhu, Yiheng, et al.
Published: (2024) -
ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings
by: Kong, Zitai, et al.
Published: (2025)