A protein model can look finished on screen and still lead an aptamer design in the wrong direction. The file may represent another isoform, omit the modification your assay depends on, or show a binding surface that disappears when the target joins its natural complex. A complete chain and an attractive 3D picture do not protect against those errors.

You do not have to be a structural bioinformatician to notice many of these problems. What matters is knowing what the coordinates describe, which parts are supported by evidence and which questions must be answered experimentally. This guide is written for molecular biologists, assay developers and researchers who commission or use structure-guided aptamer design.