3 papers
cs.LG2026
RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design
Meghana Kshirsagar, Allen Nie, Ching-An Cheng +5
We introduce RosettaSearch, an inference-time multi-objective optimization approach for backbone conditioned protein sequence design. We use large language models (LLMs) as a gener…
cs.LG2025
Improving Protein Sequence Design through Designability Preference Optimization
Fanglei Xue, Andrew Kubaney, Zhichun Guo +4
Protein sequence design methods have demonstrated strong performance in sequence generation for de novo protein design. However, as the training objective was sequence recovery, it…
q-bio.BM2025
SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation
Fanglei Xue, Meihan Zhang, Shuqi Li +5
Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered "undruggable…