This study continues our incremental work on recommendations for DL models regarding input encoding and control of chemical series. While this study was limited to one architecture and two protein families, it provides a foundation to understand the basic behaviour of PCM models, insights on how to adjust performance metrics for a protein-wise analysis, and a first step towards exploring more general questions. Those could include architecturecentric analyses to confirm if the same trends are observed when changing the layers or the model structure, or using other protein families with a different distribution of actives ratios, which may be flat or skewed to the inactives.