OnionNet

[AbdelmoujoudFaris]

Please, why did I encounter this error on the last step to obtain the pKa after obtaining the path? error.txt

[zhenglz]

Given this error: OSError: Unable to open file (file signature not found)

It is possible that this file "models/StandardScaler.model" or "models/CNN_final_model_weights.h5" not accessible. Try absolute path to read the files.

[Kerro-junior]

Hi, I have questions about your article:

the binding affinity (pKa) of the native pose
is 2.29, whereas with OnionNet, the predicted binding affinity
based on the crystal structure and the “native-like” pose is
3.436 and 3.421, respectively. Thus, the OnionNet model is
found to be robust and insensitive to the small variations of the
ligand binding poses

What is your method to predict the native pose via 'native-like' poses?

[zhenglz]

Given the native pose (the ligand structure in the original protein-ligand complex crystal structure), OnionNet is used to predict the pkx using the protein-ligand cystal structure. For native-like pose, AutoDock Vina is used to dock the ligand into the receptor structure and the poses with low RMSD (less than 2 angstrom) to the native pose (ligand structure in the crystal structure) are "native-like" poses.