Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method.

ABSTRACT: 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

SUBMITTER: Stevenson GA 

PROVIDER: S-EPMC10647021 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature