7 citations · 17 across the 9 of their papers we have counts for
9 papers
Towards A Generative Protein Evolution Machine with DPLM-Evo
Xinyou Wang, Liang Hong, Jiasheng Ye +4
Proteins are shaped by gradual evolution under biophysical and functional constraints. Protein language models learn rich evolutionary constraints from large-scale sequences, and d…
Protein Autoregressive Modeling via Multiscale Structure Generation
Yanru Qu, Cheng-Yen Hsieh, Zaixiang Zheng +2
We present protein autoregressive modeling (PAR), the first multi-scale autoregressive framework for protein backbone generation via coarse-to-fine next-scale prediction. Using the…
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…