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UnixJunkie / molenc

MolEnc: a molecular encoder using rdkit and OCaml.
BSD 3-Clause "New" or "Revised" License
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support atom pairs in 3D #79

Closed UnixJunkie closed 4 years ago

UnixJunkie commented 4 years ago

very interesting encoding in there "Zhu, F., Zhang, X., Allen, J. E., Jones, D., & Lightstone, F. C. (2020). Binding Affinity Prediction by Pairwise Function Based on Neural Network. Journal of Chemical Information and Modeling." https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00026

UnixJunkie commented 4 years ago

Their atom type is almost: (partial-charge, VdW-radius, LJ-epsilon)

UnixJunkie commented 4 years ago

but the simplest way for us is to change bond distance in each atom pair to Euclidian distance. Then, in the Tanimoto, we need to use a triangle kernel function whose bandwidth has been optimized on a given dataset in some way.

UnixJunkie commented 4 years ago

test on a pre-docking experiment: does this improve the regressor performance compaired to working only in 2D

UnixJunkie commented 4 years ago

Since we need to vectorize the output, the triangular kernel is not acceptable. We can use linear binning or an histogram with overlaping bins.

UnixJunkie commented 4 years ago

giving up; this is just annoying