Publications (5)
Protein Conformation Generation via Force-Guided SE(3) Diffusion Models
Yan Wang, Lihao Wang, Yuning Shen +4
The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as m…
Learning Harmonic Molecular Representations on Riemannian Manifold
Yiqun Wang, Yuning Shen, Shi Chen +3
Molecular representation learning plays a crucial role in AI-assisted drug discovery research. Encoding 3D molecular structures through Euclidean neural networks has become the pre…
ConfRover: Simultaneous Modeling of Protein Conformation and Dynamics via Autoregression
Yuning Shen, Lihao Wang, Huizhuo Yuan +3
Understanding protein dynamics is critical for elucidating their biological functions. The increasing availability of molecular dynamics (MD) data enables the training of deep gene…
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…
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…