Ecker's research focuses on computational drug design which not only led to the identification of highly active propafenone-type inhibitors of P-glycoprotein, but also paved the way for development of new descriptors and virtual screening approaches for identification of new scaffolds active at P-gp. With the increasing knowledge on the importance of P-gp for ADME, his interest moved towards the prediction of P-gp substrate properties. Around 2010 he extended the studies also on other antitargets, such as the hERG potassium channel, as well as on the serotonin transporter, the GABA receptor and the insulin receptor.