33 papers
Exploring the Alignment of Generation and Understanding in Protein Structure Modeling
Junde Xu, Yuansheng Huang, Zijun Gao +5
Understanding and generation are often treated as two separate paradigms in training deep neural networks, despite the fact that both are trained with closely related objectives su…
SF-Cluster: Frustration-Guided MSA Subsampling for Alternative Protein Conformation Recovery
Hanqun Cao, Zijun Gao, Chunbin Gu +3
Deep-learning structure predictors are sensitive to their multiple sequence alignment (MSA) input, making MSA subsampling a practical route to recovering alternative conformations.…
Struct-Searcher: Agentic Structural Thinking Advances Multimodal Deep Information Seeking
Fan Zhang, Vireo Zhang, Shengju Qian +7
Deep research agents have attracted increasing attention for their ability to collect large-scale online information to acquire target knowledge, with recent efforts shifting from…
AlloGen: Conformation-Selective Binder Generation with Differential State Scoring
Hanqun Cao, Zachary Quinn, Aastha Pal +4
Protein binder design has largely optimized for affinity alone, leaving conformational selectivity unaddressed: for allosteric targets such as kinases, nuclear receptors, and GPCRs…
GeoCycler: Reward-Aligned 3D Diffusion for Constraint-Conditioned Cyclic Peptide Design
Jingjie Zhang, Hanqun Cao, Haosen Shi +10
Cyclic peptides are attractive therapeutic modalities because their closed-ring topology can improve stability and target specificity. However, de novo cyclic peptide design remain…
SurgLQA: Scalable Long-Horizon Surgical Video Question Answering
Diandian Guo, Xikai Yang, Ruiyang Li +2
Surgical Video Question Answering (VideoQA) provides a promising paradigm for dynamic intraoperative interpretation, enabling real-time decision support and context-aware retrieval…