Including 3D information very rarely increases the quality of the QSAR models (ligand-based), and typically introduces more noise than signal, as finding the active conformer is still quite a challenge for the scientific community.
In addition, the stereochemistry of the most active molecule is usually known in projects involving chiral molecules. Therefore, irrelevant stereoisomers can be removed from the dataset during pre-processing data preparation.
Moreover, we have observed that when the absolute configuration is not known, R-S enantiomers are assigned randomly or the molecule is depicted in its racemic form.
As these aspects are complex, company and project dependent, and typically do not improve the quality of the ligand-based model, stereo information is not taken into account in models and during generation (with the exception of generators using 3D parameters).
Nevertheless, if 3D is critical to your project, it can be taken into account through the use of Makya 3D modules. By adding a 3D score, stereoisomer enumeration can be accomplished and be taken into account in the scoring function. Please feel free to contact us regarding Makya 3D if you do not have access to these features.