DesignMaster: A Multi-Conditional Diffusion Framework for Rational PROTAC Design

doi:10.1093/bioinformatics/btag714

DesignMaster: A Multi-Conditional Diffusion Framework for Rational PROTAC Design

2026-09-24

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DOI：10.1093/bioinformatics/btag714

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Proteolysis-targeting chimeras (PROTACs) enable targeted protein degradation through ternary complex formation with E3 ubiquitin ligase. However, the rational design of PROTACs remains highly challenging due to limited structure–activity relationship data and the vast conformational diversity of linkers. Existing computational approaches can be broadly divided into structure-based ternary modelling methods and fragment-based linker generation models. Although these approaches have advanced PROTAC design, they typically neglect key physicochemical constraints and linker-length control during the generation process, causing the generated PROTACs to lack balanced structural properties required for effective ternary complex formation with drug-like characteristics.

DesignMaster: A Multi-Conditional Diffusion Framework for Rational PROTAC Design

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