Random Forest / Cross-Docking
OpenBabel (2.4.1), Smina (1.2.2), Scikit-learn (0.20.0)
Default Smina parameters
The Ligand-Target-Affinity dataset was downloaded from the BindingDB website. The BACE-1 ligands were pulled out using our in-house scripts, and the binding affinities were adopted according to the preference of kd > ki > IC50. Others such as kon and koff were not adopted. After merging similar entries and removing large ligands with more than 20 rotatable bonds, the size of ligands in the BACE-1 ligand dataset was reduced to 6754. RCSB database was used to download 261 PDB BACE-1 crystal structure. A subset of protein (representative receptors) was selected using clustering analysis. Each ligand is docked to representative receptors. The resulting scores are used to train a random forest model.
Yes
Yes