The pharmacological mechanisms of traditional Chinese medicine (TCM) are very complicated. At the molecular level

the Chinese medicine emphasizes multi-component and multi-target synergistic effects. However

the composition of the TCM is complex and it is difficult to reveal the action mechanisms of TCM. At present

there are many methods to study the pharmacological mechanisms of TCM

which are roughly divided into three models:chemistry-focused study

target-directed study

and systems-biology-based study. To some extent

these methods may illustrate mechanism of action of TCM. However

there are still some limitations. Network-based analysis is still difficult and deficient

including the biological network is extremely complex

optimization problem for module identification

the lack of dynamic and continuous quantitative researches. To effectively find the relationship among multiple targets

we propose a modular analysis framework

including module identification

optimization

similarity calculation of module structure and functional enrichment analysis. The exploration of modular structure has been proposed as a key factor to understand the complexity of drug-target networks. The method of modular analysis provides a new method for pharmacological study in future.