Closed hi7049 closed 2 years ago
Hey, you can check out the code for creating sequence based splits here: https://github.com/gnina/scripts#generating-clustered-cross-validation-splits-of-data
for ligand similarity we use tanimoto, not sequence. we consider protein similarity of 30% when ligand tanimoto similarity is greater than 0.9
In the "Data sets and Preprocessing" section of your paper, you mention that " we removed all proteins from the training set that had either sequence identity greater than 50% or ligand similarity greater than 0.9 and sequence identity greater than 30%".