Synthetic and biological nanopores can be used for fundamental and applied studies of individual biomolecules in high throughput. By measuring resistive current pulses during the translocation of single molecules through an electrolyte-filled nanopore, this technique can characterize the size, conformation, assembly, and activity of hundreds of unlabeled molecules within seconds. Inspired by the olfactory sensilla of insect antennae, we demonstrate that coating nanopores with a fluid lipid bilayer considerably extends the capabilities of nanopore-based assays. For instance, coating nanopores with different lipids allows fine control of the surface chemistry and diameter of nanopores. Incorporation of mobile ligands in the lipid bilayer imparts specificity to the nanopore for targeting proteins and introduces control of translocation times for targeted proteins based on their net electric charge. Most recently, we explored the potential of this technique for determining the affinity constant of a protein-ligand interaction, monitoring the kinetics of binding of this interaction, characterizing the aggregation state of Alzheimer’s disease-related amyloid peptides, and determining the molecular shape of individual proteins.