DegradeQuery: Counterfactual Tuple Pretraining for Context-Aware PROTAC Degradation Prediction
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 molecule and its biological context. Although public databases contain thousands of structured molecule-target-E3 records, degradation measurements are available for only a small fraction of them. Existing supervised approaches therefore leave most recorded chemical-biological relationships unused. We introduce DegradeQuery, a context-aware prediction framework that converts these label-missing records into a pretraining signal. Its counterfactual tuple pretraining objective contrasts recorded tuples with alternati...
| Authors | Dong Xu, Zhangfan Yang, Jiantao Wu et al. |
|---|---|
| Primary category | q-bio.BM |
| Published | 11 August 2026 |
| Last updated at source | 11 August 2026 |
Silytics shows public metadata from arXiv and links to the original. Information may be incomplete or out of date. Last refreshed 17 October 2026. Licenses and terms of the original apply to the work itself. Not financial, legal or professional advice.