18 citations · 35 across the 10 of their papers we have counts for
10 papers
AMix-2: Establishing Protein as a Native Modality in Large Language Models
Keyue Qiu, Yixin Wu, Lihao Wang +19
We present AMix-2, a protein-text foundation model that establishes protein as a native modality in large language models (LLMs), unifying protein understanding and sequence design…
AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model
Changze Lv, Jiang Zhou, Siyu Long +22
We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws,…
Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling
Xiangxin Zhou, Mingyu Li, Yi Xiao +5
Cyclic peptides offer inherent advantages in pharmaceuticals. For example, cyclic peptides are more resistant to enzymatic hydrolysis compared to linear peptides and usually exhibi…
An All-Atom Generative Model for Designing Protein Complexes
Ruizhe Chen, Dongyu Xue, Xiangxin Zhou +3
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has bee…
Elucidating the Design Space of Multimodal Protein Language Models
Cheng-Yen Hsieh, Xinyou Wang, Daiheng Zhang +5
Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design.…
ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design
Yiming Ma, Fei Ye, Yi Zhou +3
Nature creates diverse proteins through a 'divide and assembly' strategy. Inspired by this idea, we introduce ProteinWeaver, a two-stage framework for protein backbone design. Our…
DPLM-2: A Multimodal Diffusion Protein Language Model
Xinyou Wang, Zaixiang Zheng, Fei Ye +3
Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living org…
ProteinBench: A Holistic Evaluation of Protein Foundation Models
Fei Ye, Zaixiang Zheng, Dongyu Xue +7
Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D…
Antigen-Specific Antibody Design via Direct Energy-based Preference Optimization
Xiangxin Zhou, Dongyu Xue, Ruizhe Chen +3
Antibody design, a crucial task with significant implications across various disciplines such as therapeutics and biology, presents considerable challenges due to its intricate nat…
Diffusion Language Models Are Versatile Protein Learners
Xinyou Wang, Zaixiang Zheng, Fei Ye +3
This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequen…