PROTAC-DB 4.0: an expanded knowledgebase of targeted protein degradation modalities with AI-powered knowledge discovery
Related Experiment Video
Updated: Nov 1, 2026

High-Throughput Cellular Profiling of Targeted Protein Degradation Compounds Using HiBiT CRISPR Cell Lines
Published on: November 9, 2020
Jingxuan Ge1,2, Chen Yin3, Yurong Li1
1College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang, China.
Abstract:
Proteolysis-targeting chimeras (PROTACs) represent an emerging therapeutic modality that harnesses the ubiquitin-proteasome system to induce targeted protein degradation (TPD). Their event-driven and catalytic mechanisms provide new opportunities to target previously undruggable proteins. However, the rapid expansion of TPD technologies, including molecular glues (MGs) and X-functional targeting chimeras (XTACs), together with the increasing application of artificial intelligence (AI) in degrader design, highlights the need for comprehensive and continuously updated data resources. Here, we present PROTAC-DB 4.0, an expanded knowledgebase covering major targeted degradation and induced-proximity technologies. Compared with the previous version, PROTAC-DB 4.0 contains 15 502 PROTAC entries, together with 24 798 MG entries and 272 XTAC entries, with expanded experimental annotations, patent-derived compounds, and modality-specific data fields. A major advancement in PROTAC-DB 4.0 is the integration of a large language model and retrieval-augmented generation-based natural language query system, which connects structured database records with scientific literature to enable intuitive knowledge discovery across PROTACs, MGs, and XTACs. By combining comprehensive data curation with AI-assisted information retrieval, PROTAC-DB 4.0 provides an accessible platform to support degrader discovery, data-driven modeling, and rational design of next-generation targeted degradation and induced-proximity therapeutics. PROTAC-DB 4.0 is freely accessible at http://cadd.zju.edu.cn/protacdb/.
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07:22The Development and Application of Biophysical Assays for Evaluating Ternary Complex Formation Induced by Proteolysis Targeting Chimeras (PROTACS)
Published on: January 12, 2024
10:44Chemical Inactivation of the E3 Ubiquitin Ligase Cereblon by Pomalidomide-based Homo-PROTACs
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