CHARMM-GUI <i>EnzyDocker</i> for Protein-Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes.

ABSTRACT: Enzymes play crucial roles in all biological systems by catalyzing a myriad of chemical reactions. These reactions range from simple one-step processes to intricate multistep cascades. Predicting mechanistically appropriate binding modes along a reaction pathway for substrate, product, and all reaction intermediates and transition states is a daunting task. To address this challenge, special docking programs like EnzyDock have been developed. Yet, running such docking simulations is complicated due to the nature of multistep enzyme processes. This work presents CHARMM-GUI EnzyDocker, a web-based cyberinfrastructure designed to streamline the preparation and running of EnzyDock docking simulations. The development of EnzyDocker has been achieved through integration of existing

SUBMITTER: Suh D 

PROVIDER: S-EPMC11866752 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature