I have a set of virtual screening hits and want to create “representation vectors” for ligands (L) and ligand-protein interactions (LP) using DeepChem GraphConv.
How can I create representation vectors for L and LP using GraphConv? Can you recommend any tutorial-like material for that? It would be great if you could share pipelines you use for creating the vectors of protein-ligand interactions.
Then, I aim to use these vectors, individually (L, LP) or combined (L+LP), as input for an unsupervised clustering task. So, I want to use the representation vectors for clustering the compounds instead of classifying them. Do you think they are suitable for clustering tasks?