chengwang88/deltavina

DeltaVina scoring function

deltavina's Issues

ΔvinaRF20 as an custom scoring fuction in gnina

Hi Cheng,

Thanks for the great work.

I want to use ΔvinaRF20 together with the CNNScore from gnina, which is a fork of smina

Since smina and gnina allows the use of custom scoring function, I wonder if ΔvinaRF20 could be employed as a custom scoring function for gnina.

This is an example of a custom fuction file: https://github.com/gnina/gnina/blob/master/examples/kitchensink.score

Thank you very much.

Best regards,

Hien

rffit creation and response y used

Dear chengwang88,

thanks for the tool, I was going to test the feature set and response with another method.

I noticed that the rffit model of randomForest is provided and can be used to make new predictions. However, I would be also interested in the part that creates rffit in particular the y response variable (output value). In the associated paper from 2017 [1], it is stated that this is delta pKd(train), which is equal to pKd(train) - pKd(VINA). If pKd(VINA) is the score from Vina, could you please let me know what pKd(train) corresponds to? I have trouble tracking down this variable. I'd like to make sure to use the same response as yours such that I can make a fair comparison. Many thanks in advance.

[1] Cheng Wang 1 and Yingkai Zhang (2017). Improving Scoring-Docking-Screening Powers of Protein-Ligand Scoring Functions using Random Forest.