Nature's blueprint to signaling-decoupled GPCR endocytosis - MD simulations

# Nature's blueprint to signaling-decoupled GPCR endocytosis - MD simulations This repository contains the molecular dynamics (MD) simulation data used in the manuscript: "Nature's blueprint to signaling-decoupled GPCR endocytosis" ## Contents The dataset includes raw topology files (.gro) and trajectory files (.xtc) for each system analyzed in the study after minimization and equilibration. The initial input files for system setup using CHARMM-GUI are also provided. Additionally included are protein-centered topology files (.pdb) and trajectory files (.dcd) for all replicas, as well as a renumbered version of the receptor chain used as MDPath input. The systems used for the creation of the dynophore figure, based on ligand-centered structures, are also provided. Each simulation subdirectory is organized by:- Active/Inactive state- Protein/Ligand ## Directory Structure Supporting_Material/├── AT1R active/├── AT1R inactive/└── README ## Example File Naming For the AngII-bound system:- Input file for CHARMM-GUI setup: `AT1R_with_ANGII_prepared`- Corresponding replica files are located within each subdirectory ## Usage These data files can be used to:- Reproduce the analyses in the manuscript- Perform additional studies based on this data