9 papers
Scalable Peptide Design via Memory-Efficient Equivariant Transformer
Rui Jiao, Xiangzhe Kong, Yinjun Jia +4
Target-specific peptide design requires sequence and structure co-design under full atom geometric constraints. Latent generative frameworks offer an effective route for this probl…
h-MINT: Modeling Pocket-Ligand Binding with Hierarchical Molecular Interaction Network
Yanru Qu, Yijie Zhang, Wenjuan Tan +6
Accurate molecular representations are critical for drug discovery, and a central challenge lies in capturing the chemical environment of molecular fragments, as key interactions,…
From Macro to Micro: Benchmarking Microscopic Spatial Intelligence on Molecules via Vision-Language Models
Zongzhao Li, Xiangzhe Kong, Jiahui Su +8
This paper introduces the concept of Microscopic Spatial Intelligence (MiSI), the capability to perceive and reason about the spatial relationships of invisible microscopic entitie…
Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding
Xinheng He, Yijia Zhang, Haowei Lin +4
Structure-based drug design has seen significant advancements with the integration of artificial intelligence (AI), particularly in the generation of hit and lead compounds. Howeve…
Latent Retrieval Augmented Generation of Cross-Domain Protein Binders
Zishen Zhang, Xiangzhe Kong, Wenbing Huang +1
Designing protein binders targeting specific sites, which requires to generate realistic and functional interaction patterns, is a fundamental challenge in drug discovery. Current…
Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints
Dapeng Jiang, Xiangzhe Kong, Jiaqi Han +6
Cyclic peptides, characterized by geometric constraints absent in linear peptides, offer enhanced biochemical properties, presenting new opportunities to address unmet medical need…