darrenwee / drug-discovery Goto Github PK

Might only need the hydrophobic descriptor (as suggested in the project handout)

This link https://drive.google.com/open?id=16criDpuQpCSX-jqosoUxj4uQFZhyIBYr is not working. I am wondering if you could fix it.

Also, could you please let us know how did you repair the pdbbind dataset that is used for kdeep model? Thanks.

Implement a (simplified) version of the voxel feature extraction

Ref: https://github.com/Acellera/htmd/blob/master/htmd/molecule/voxeldescriptors.py

Both protein and ligand are featurized via a voxelized 24 Å representation of the binding site considering eight pharmacophoric-like properties.

Jiménez, J., Skalic, M., Martínez-Rosell, G., & De Fabritiis, G. (2018). K DEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks. Journal of chemical information and modeling, 58(2), 287-296.

Rebuild a .pdb file with just the atoms and (x, y, z) positions, and see if the output is the same when generating the voxeldescriptors with htmd.