DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Models
Designing small molecule ligands that bind with high affinity to specific protein pockets is a fundamental goal in drug discovery, as small molecules constitute a major fraction of approved therapeutics. Recent breakthroughs in structure prediction, such as AlphaFold-3 and Boltz-2, enable accurate biomolecular interaction prediction and show promise as foundation models for downstream tasks, including binding affinity prediction. We propose to leverage these models and introduce DBMol, a new structure predictor-guided framework for de novo small molecule design. DBMol formulates an alternating optimization and projection process. In the optimization stage, DBMol starts from an initial mol...
| Authors | Yiming Qin, Kai Yi, Miruna Cretu et al. |
|---|---|
| Primary category | cs.LG |
| Published | 21 July 2026 |
| Last updated at source | 21 July 2026 |
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