Experimental Ki values of active, inactive and unspecified compounds found in ChEMBL.
Note that the non-inactive compounds of these 1,528 bioassays include the inconclusive and unspecified compounds as well as the active compounds.
Vermicompost has been considered as a material containing plant growth promoting compounds including enzymes, different hormones and so many other unspecified compounds (Atiyeh et al. 2002).
Supplementary figures and tables that summarize the results from the 843 assays that have active compounds only (without any inconclusive or unspecified compounds).
The reason for using the non-inactive compounds instead of the active compounds in our analysis is that the inconclusive and unspecified compounds are indeed active in many assays.
As described in the Methods section, the same analyses were also performed for a subset of the 1,528 assays, which consists of 843 assays that have active compounds only (without any inconclusive or unspecified compounds), and the results are summarized in Additional file 4. Note the minor peaks in the distributions for the best-conformer-pair approach in Figures 9, 10.
Therefore, a subset of the 1,528 assays were generated by selecting 843 assays which have active compounds only (without any inconclusive or unspecified compounds), and the same analyses were performed both for the 1,528 assay set and the 843 assay set.
For example, the unspecified compounds in some assays in Table 5 do have AhR agonist activities (given in fold induction of AhR expression compared to the untreated controls), but the assay contributor did not explicitly specify whether they are active or inactive.
The reason for using non-inactive compounds instead of active compounds is that the unspecified and inconclusive compounds are indeed active in many assays.
The reason for considering non-inactive compounds, rather than active compounds, in the SAR clustering is that, in many assays, the unspecified and inconclusive compounds are indeed active in many assays.
