- Stevenson, Garrett;
- Kirshner, Dan;
- Bennion, Brian;
- Yang, Yue;
- Zhang, Xiaohua;
- Zemla, Adam;
- Torres, Marisa;
- Epstein, Aidan;
- Jones, Derek;
- Kim, Hyojin;
- Bennett, W;
- Wong, Sergio;
- Allen, Jonathan;
- Lightstone, Felice
Protein-ligand interactions are essential to drug discovery and drug development efforts. Desirable on-target or multitarget interactions are the first step in finding an effective therapeutic, while undesirable off-target interactions are the first step in assessing safety. In this work, we introduce a novel ligand-based featurization and mapping of human protein pockets to identify closely related protein targets and to project novel drugs into a hybrid protein-ligand feature space to identify their likely protein interactions. Using structure-based template matches from PDB, protein pockets are featured by the ligands that bind to their best co-complex template matches. The simplicity and interpretability of this approach provide a granular characterization of the human proteome at the protein-pocket level instead of the traditional protein-level characterization by family, function, or pathway. We demonstrate the power of this featurization method by clustering a subset of the human proteome and evaluating the predicted cluster associations of over 7000 compounds.