9 papers
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…
Scalable Spatio-Temporal SE(3) Diffusion for Long-Horizon Protein Dynamics
Nima Shoghi, Yuxuan Liu, Yuning Shen +3
Molecular dynamics (MD) simulations remain the gold standard for studying protein dynamics, but their computational cost limits access to biologically relevant timescales. Recent g…
Decomposed Direct Preference Optimization for Structure-Based Drug Design
Xiwei Cheng, Xiangxin Zhou, Yuwei Yang +2
Diffusion models have achieved promising results for Structure-Based Drug Design (SBDD). Nevertheless, high-quality protein subpocket and ligand data are relatively scarce, which h…
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.…
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…