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cs.CE2026
CODesign: Consistency from Data to Trajectory in All-Atom Protein Binder Co-Design
Yuanle Mo, Bo Qiang, Haitao Lin +4
The central challenge in de novo protein design is generating plausible, mutually compatible structures and sequences, such that each designed sequence folds into its intended stru…
cs.CE2026
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…
cs.CE2026
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…