Control of fluorescent dye localization in live cells is crucial for fluorescence imaging.
Here, we describe quantitative structure activity relation (QSAR) models for predicting intracellular
localization of fluorescent dyes. For generating the QSAR models, electric charge (Z) calculated by pKa, conjugated bond
number (CBN), the largest conjugated fragment (LCF), molecular weight (MW) and log P were used as parameters. We
identified the intracellular localization of 119 BODIPY dyes in live NIH3T3 cells, and assessed the accuracy of our
models by comparing their predictions with the observed dye localizations. As predicted by the models, no BODIPY dyes
localized in nuclei or plasma membranes. The accuracy of the model for localization in fat droplets was 92%, with the
models for cytosol and lysosomes showing poorer agreement with observed dye localization, albeit well above chance
levels. Overall therefore the utility of QSAR models for predicting dye localization in live cells was clearly demonstrated.