Kdeep-maxalign
Kdeep
Kdeep was trained on PDBbind database.
After docking the ligands with their most similar cocrystals using rDock tethered docking,
we inputed the resulting pose and the protein to Kdeep.
Kdeep is a convolutional neural network trained on PDBind database which predicts affinity values based
on the pose of the ligand and the protein.
No
Maximum similarity substructure alignment
HTMD/RDKit/rDock
Tautomers and different conformers considered with RDKit
Proteins were prepared using proteinPrepare from HTMD
Different conformers and tautomers were considered using RDKit,
proteins were prepared using proteinPrepare from HTMD
proteinPrepare default parameters
For each problem ligand, the most similar cocrystallized ligand was used to perform an structural based
alignment using rDock tethered docking.
No
Yes