  In cheminformatics, network representations of the space of compounds have
been suggested extensively. Among these, the threshold-network consists of
nodes representing molecules. In this network representation, two molecules are
connected by a link if the Tanimoto coefficient, a similarity measure, between
them exceeds a preset threshold. However, the topology of the threshold-network
is affected significantly by the preset threshold. In this study, we collected
the data of biologically relevant compounds and bioactivities. We defined the
weighted network where the weight of each link between the nodes equals the
Tanimoto coefficient between the bioactive compounds (nodes) without using the
threshold. We investigated the relationship between the strength of the link
connection and the bioactivity closeness in the weighted networks. We found
that compounds with significantly high or low bioactivity have a stronger
connection than those in the overall network.
