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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:

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