How to encode proteins in the PDBbind task?

[fanxiaoyu0]

Very enlightening work. Congratulations on your great achievements in the OGB Challenge! In addition, I noticed that you have made fine-tuning on the PDBbind dataset. How should you encode the protein information? Because proteins usually contain more heavy atoms, do you directly use Transformer-M to encode proteins?

[1874Mercury]

Also looking forward to the answer to this question...

[lsj2408]

It is a good catch! For the PDBBind task, each data instance is a protein-ligand complex. Since the size of a protein is much larger than that of a ligand, each protein-ligand complex only contains the protein atoms around the ligand. Thus, the model receives the complex as input and predicts its binding affinity.