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Table 3 Evaluation methods for in silico models

From: A proposed framework for the systematic review and integrated assessment (SYRINA) of endocrine disrupting chemicals

Modeling type Description of the method
For all modeling work: ▪ 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: ▪ Use of sufficiently diverse training set covering the EDC compound domain of interest
▪ Use of sufficiently diverse external test set covering the EDC compound domain of interest should be used
▪ 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
▪ Sufficient statistical quality achieved
▪ Consistent applicability domain established, e.g. using a conformal prediction framework
For ligand based pharmacophore models: ▪ Use of sufficiently diverse training set covering the EDC compound mechanism/domain of interest
▪ All training set compounds should, approximately, fit the derived model equally well unless there are demonstrable differences in the binding affinity
▪ Use of sufficiently diverse external test set that covers the EDC compound domain of interest to demonstrate generalizability
Protein structure based models: ▪ Several protein structures should be used to account for flexibility of the protein covering relevant conformations
▪ Use of sufficiently diverse training set covering the EDC compound domain of interest
▪ Consensus docking and scoring to ensure robustness and stability of results
▪ Use of sufficiently diverse external test set covering the EDC compound domain of interest