Protein

Molecular therapeutics. Broader than protein-only work: drug-target binding and polypharmacy side effects both live here. 3 tutorials.

Drug-target affinity prediction with DeepDTA

Draft

Predict binding affinity between compounds and protein targets by encoding SMILES strings and amino-acid sequences with parallel CNNs, on three BindingDB subsets (Kd, IC50, Ki).

intermediate · ~1 h on one GPU

Drug-target affinity prediction with DeepDTA

Drug-target interaction prediction with DrugBAN

Draft

An interpretable bilinear attention network over drug molecular graphs and protein sequences, with optional domain adaptation for cross-domain generalisation on BindingDB and BioSNAP.

advanced · ~2 h on one GPU

Drug-target interaction prediction with DrugBAN

Polypharmacy side effect prediction with GripNet

Draft

Link prediction on a protein-drug knowledge graph. GripNet propagates messages along a task-specific path over a supergraph to predict side effects caused by drug combinations.

advanced · ~15 min on one GPU

Polypharmacy side effect prediction with GripNet