DockEM: an enhanced method for atomic-scale protein-ligand docking refinement leveraging low-to-medium resolution cryo-EM density maps.

ABSTRACT: Protein-ligand docking plays a pivotal role in virtual drug screening, and recent advancements in cryo-electron microscopy (cryo-EM) technology have significantly accelerated the progress of structure-based drug discovery. However, the majority of cryo-EM density maps are of medium to low resolution (3-10 Å), which presents challenges in effectively integrating cryo-EM data into molecular docking workflows. In this study, we present an updated protein-ligand docking method, DockEM, which leverages local cryo-EM density maps and physical energy refinement to precisely dock ligands into specific protein binding sites. Tested on a dataset of 121 protein-ligand compound, our results demonstrate that DockEM outperforms other advanced docking methods. The strength of DockEM lies in its ability t

SUBMITTER: Zou J 

PROVIDER: S-EPMC11891657 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature