BATMAN-TCM 2.0: an enhanced integrative database for known and predicted interactions between traditional Chinese medicine ingredients and target proteins

Abstract Traditional Chinese medicine (TCM) is increasingly recognized and utilized worldwide. However, the complex ingredients of TCM and their interactions with the human body make elucidating molecular mechanisms challenging, which greatly hinders the modernization of TCM. In 2016, we developed B...

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Bibliographic Details
Published in:Nucleic acids research 2024-01, Vol.52 (D1), p.D1110-D1120
Main Authors: Kong, Xiangren, Liu, Chao, Zhang, Zuzhen, Cheng, Meiqi, Mei, Zhijun, Li, Xiangdong, Liu, Peng, Diao, Lihong, Ma, Yajie, Jiang, Peng, Kong, Xiangya, Nie, Shiyan, Guo, Yingzi, Wang, Ze, Zhang, Xinlei, Wang, Yan, Tang, Liujun, Guo, Shuzhen, Liu, Zhongyang, Li, Dong
Format: Article
Language:English
Subjects:
Databases, Pharmaceutical
Drugs, Chinese Herbal - chemistry
Humans
Medicine, Chinese Traditional
Network Pharmacology
Proteins
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Summary:Abstract Traditional Chinese medicine (TCM) is increasingly recognized and utilized worldwide. However, the complex ingredients of TCM and their interactions with the human body make elucidating molecular mechanisms challenging, which greatly hinders the modernization of TCM. In 2016, we developed BATMAN-TCM 1.0, which is an integrated database of TCM ingredient–target protein interaction (TTI) for pharmacology research. Here, to address the growing need for a higher coverage TTI dataset, and using omics data to screen active TCM ingredients or herbs for complex disease treatment, we updated BATMAN-TCM to version 2.0 (http://bionet.ncpsb.org.cn/batman-tcm/). Using the same protocol as version 1.0, we collected 17 068 known TTIs by manual curation (with a 62.3-fold increase), and predicted ∼2.3 million high-confidence TTIs. In addition, we incorporated three new features into the updated version: (i) it enables simultaneous exploration of the target of TCM ingredient for pharmacology research and TCM ingredients binding to target proteins for drug discovery; (ii) it has significantly expanded TTI coverage; and (iii) the website was redesigned for better user experience and higher speed. We believe that BATMAN-TCM 2.0, as a discovery repository, will contribute to the study of TCM molecular mechanisms and the development of new drugs for complex diseases. Graphical Abstract Graphical Abstract
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkad926