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Background  The sentence of “Danshen (Salvia Miltiorrhizae Radix et Rhizoma) and Siwu decoction are similar in function” was first recorded in an ancient Chinese medical book “Fu Ren Ming Li Lun”. This theory has far-reaching influence on the clinical practice of Chinese medicine and is highly respected by Chinese medical doctors. However, the theory has limitations and controversial part for there is no in-depth and system comparative study.    Methods  We collected the molecular structures of 129 compounds of Danshen and 81 compounds of Siwu decoction from the literatures. MACCS fingerprints and Tanimoto similarity were calculated based on the molecular structures for comparing the structural feature. Molecular descriptors which represent physical and chemical properties were calculated by Discovery Studio. Principal component analysis (PCA) of was performed based on the descriptors. The ADMET properties were predicted by FAF-Drugs4. The effect targets for the compounds with good ADMET properties were confirmed from experimental data and predicted using the algorithm comprising Bernoulli Naive Bayes profiling.    Results  Based on the molecular structures, the presented study compared the structural feature, physical and chemical properties, ADMET properties, and effect targets of compounds of Danshen and Siwu decoction. It is found that Danshen and Siwu decoction do not have the same main active components. Moreover, the 2D structure of compounds from Danshen and Siwu decoction is not similar. Some of the compounds of Danshen and Siwu decoction are similar in 3D structure. The compounds with good ADMET properties of Danshen and Siwu decoction have same predicted targets, but some have different targets.    Conclusions  It can be inferred from the result that Danshen and Siwu decoction have some similarities, but also present differences from each other in the structure of the compounds and predicted targets. This may be the material basis of the similar and different traditional efficacy of Danshen and Siwu decoction. The setence of “ Danshen and Siwu decoction are similar in function. “ which is used in clinical has its material basis and target connotation to some extent. However, the traditional effects of Danshen and Siwu decoction are not exactly the same.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12906-021-03209-1.

Comparative study of Danshen and Siwu decoction based on the molecular structures of the components and predicted targets