Modeling type | Description of the method |
---|---|
For all modeling work: | â–ª Standardization and curation of the investigated dataset to ensure consistency. This should include a clearly-stated method (including inclusion and exclusion criteria) for curation of the data and a review of the rules applied to chemical structures in order to ensure standardization |
QSAR models: | â–ª Use of sufficiently diverse training set covering the EDC compound domain of interest |
â–ª Use of sufficiently diverse external test set covering the EDC compound domain of interest should be used | |
â–ª Assembly of internal and external validation, i.e. several internal and external validation sets, and models created in a double loop fashion, followed by consensus predictions | |
â–ª Sufficient statistical quality achieved | |
â–ª Consistent applicability domain established, e.g. using a conformal prediction framework | |
For ligand based pharmacophore models: | â–ª Use of sufficiently diverse training set covering the EDC compound mechanism/domain of interest |
â–ª All training set compounds should, approximately, fit the derived model equally well unless there are demonstrable differences in the binding affinity | |
â–ª Use of sufficiently diverse external test set that covers the EDC compound domain of interest to demonstrate generalizability | |
Protein structure based models: | â–ª Several protein structures should be used to account for flexibility of the protein covering relevant conformations |
â–ª Use of sufficiently diverse training set covering the EDC compound domain of interest | |
â–ª Consensus docking and scoring to ensure robustness and stability of results | |
â–ª Use of sufficiently diverse external test set covering the EDC compound domain of interest |