Notice the file contains two tables: we will use TrainingSet to build the 3D QSAR model and testset table to test the model. Right click on qsar_apf_example.icb and choose "Save Link As". cut and paste the address into a web browser. Step 1: Download and open the prepared ICM file. It is usually recommended to Convert the IC50 to pIC50 (-LogIC50) Template ligands from the PDB is the ideal scenario because it provides confidence in the conformation but if you do not have this you can use the best superposition for your lead compounds using the superimpose options described here. In this example we have 8 THRA inhibitors from the PDB already superimposed and we will superimpose our training set and test set onto those. Both the test set and training set relies on 3D superimposed chemicals. The example uses experimental pKd values from ChEMBL for the training set - the pKd values are also listed for the external test set so you can compare how good the model is. In this example we build a 3D QSAR model based on a set of Thyroid Hormone Receptor Alpha (THRA) inhibitors using Atomic Property Fields (APF). Induced Fit (Flexibility) Docking Tutorials
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