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DegradeQuery: Counterfactual Tuple Pretraining for Context-Aware PROTAC Degradation Prediction
Dong Xu, Zhangfan Yang, Jiantao Wu +3
Proteolysis-targeting chimeras (PROTACs) induce protein degradation by recruiting a target protein to an E3 ubiquitin ligase, making degradation a joint outcome of the degrader mol…
BioLM-Score: Language-Prior Conditioned Probabilistic Geometric Potentials for Protein-Ligand Scoring
Zhangfan Yang, Baoyun Chen, Dong Xu +4
Protein-ligand scoring is a central component of structure-based drug design, underpinning molecular docking, virtual screening, and pose optimization. Conventional physics-based e…
FROGENT: An End-to-End Full-process Drug Design Multi-Agent System
Qihua Pan, Dong Xu, Qianwei Yang +5
Drug discovery is a complex, multi-step pipeline that remains heavily dependent on manual, experience-driven operations; meanwhile, existing customized artificial intelligence tool…
READ: A Retrieval-Alignment Diffusion Framework for Structure-based Drug Design
Dong Xu, Zhangfan Yang, Junchuang Cai +4
Structure-based drug design (SBDD) models are central to modern pharmaceutical research, enabling the rational exploration of protein-ligand interactions at atomic resolution. Howe…