Abstract
Chemical space is the space of possible molecules. Investigating the structure of the space can help us exploring compounds with desirable properties. In a previous study, a network representation of the biologically relevant chemical space was suggested. The network consisted of nodes representing compounds, and a link between two nodes was drawn if the similarity between these compounds exceeds the preset threshold. However, the network topology depends on the threshold. In our study, instead of using threshold, we investigated the weighted network where the weight of a link equals similarity between two compounds. In this study, we examined bioactive compounds, whose data are from the ChEMBL database. By analyzing the weighted network of bioactive compounds for each target, we found that each network has the homogeneous structure, where rare nodes are connected to others with extreme weights. The community structure of each network was also weak. However, some detected communities were regarded as connecting tightly and exhibited the biased bioactivity distribution against the whole network. Furthermore, we found that compounds with significantly high/low bioactivity are connected strongly to each other.
