11 papers
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…
SLSREC: Self-Supervised Contrastive Learning for Adaptive Fusion of Long- and Short-Term User Interests
Wei Zhou, Yue Shen, Junkai Ji +5
User interests typically encompass both long-term preferences and short-term intentions, reflecting the dynamic nature of user behaviors across different timeframes. The uneven tem…
Toward Closed-loop Molecular Discovery via Language Model, Property Alignment and Strategic Search
Junkai Ji, Zhangfan Yang, Dong Xu +4
Drug discovery is a time-consuming and expensive process, with traditional high-throughput and docking-based virtual screening hampered by low success rates and limited scalability…
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…
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…
RIGA-Fold: A General Framework for Protein Inverse Folding via Recurrent Interaction and Geometric Awareness
Sisi Yuan, Jiehuang Chen, Junchuang Cai +4
Protein inverse folding, the task of predicting amino acid sequences for desired structures, is pivotal for de novo protein design. However, existing GNN-based methods typically su…