eLife Assessment
This important study builds on previous work from the same authors to present a conceptually distinct workflow for cryo-EM reconstruction that uses 2D template matching to enable high-resolution structure determination of small (sub-50 kDa) protein targets. The paper provides convincing evidence that the density for small-molecule ligands bound to such targets can be reconstructed without these ligands being present in the template, and it provides an insightful quantification of the level of model bias that remains in the resulting reconstructions. The convenient visualisation of small molecules bound to protein targets of a known structure will be relevant for the pharmaceutical industry.