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dbPTH: A Comprehensive Database for Protein Targets of Herbal Ingredients
Jianzhen Peng1,2, Xinhe Huang2, Kuo Yang3
1School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China.
Genomics, Proteomics & Bioinformatics
|June 8, 2026
Summary
We developed dbPTH 1.0, a comprehensive database of herbal ingredient-target interactions (ITIs). It contains over 165,000 experimentally verified ITIs, significantly expanding upon existing resources for drug discovery.
Area of Science:
- Pharmacology and Bioinformatics
- Drug Discovery and Development
- Computational Biology
Background:
- Understanding herbal ingredient-target interactions (ITIs) is crucial for herbal pharmacology and drug development.
- Existing databases lack comprehensive, experimentally verified ITI data.
- A need exists for an integrated resource to explore herb-target relationships.
Purpose of the Study:
- To develop and present dbPTH 1.0, a comprehensive database of protein targets of herbal ingredients.
- To provide a significantly expanded collection of experimentally verified ITIs compared to existing databases.
- To facilitate research in herbal pharmacology, target discovery, and pharmaceutical design.
Main Methods:
- Compiled 165,967 experimentally identified ITIs across 27,981 protein targets and 4856 ingredients from 8 species.
- Computationally identified potential orthologs in 1138 eukaryotic species, predicting over 36 million ITIs.
- Classified ingredients into 65 chemical subtypes and targets into 9 protein subgroups, with extensive annotation from 110 public resources.
Main Results:
- dbPTH 1.0 contains 165,967 experimentally verified ITIs, a substantial increase over existing databases (e.g., 41.81-fold over TCMSP).
- The database includes potential ITIs for over 2.6 million targets across 1138 species.
- Rich annotations cover 14 aspects, including genetic variation, disease association, and biological pathways, particularly for human targets.
Conclusions:
- dbPTH 1.0 is a valuable, large-scale resource for understanding herbal ingredient pharmacology.
- The database significantly enhances the scope of known experimentally verified ITIs.
- dbPTH 1.0 supports further pharmaceutical design and drug discovery efforts.
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