Conformation has a key role in the mechanism of interaction between small molecules and biological receptors. However, encoding this type of information in molecular descriptors for the construction of robust quantitative structure–activity relationships (QSAR) models is not an easy task and, so far, the dependence of these models on such feature has not been thoroughly investigated. In the present study, the authors explore the effects of conformational information on a 3D-QSAR technique by comparing models built with descriptors that encode fully described tridimensional aspects (structures docked inside a biological target), with descriptors in which this information is suppressed (flat structures) or not fully described (structures with quantum-chemically optimized geometries). As a result, the validation parameters indicate that the robustness of the models seems to be more related to the alignment aspect of the structures than to how well their tridimensional features are described.