MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations - Test Cases

MDPath Test Cases Dataset This repository contains the molecular dynamics (MD) simulation data used in the manuscript: "MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations" https://doi.org/10.1021/acs.jcim.5c01590 Contents The dataset includes post-processed topology files (.pdb) and trajectory files (.dcd) for each system analyzed in the study. Simulations were conducted for 200 ns and repeated in triplicate for statistical robustness. Each simulation subdirectory is organized by: - Protein target - Functional state (e.g., active/inactive) - Bound ligand Replicate runs are labeled numerically (1, 2, 3) in the filenames, corresponding to: - rep<number>_protein_state_ligand_top.pdb: topology file of the system - rep<number>_protein_state_ligand_traj.dcd: trajectory file of the system Directory Structure MDPath_test_cases/├── MOR/│ ├── active_DAMGO/│ └── inactive_alvimopan/├── AA2a/│ ├── active_adenosine/│ └── inactive_caffine/├── ABL1/├── ß2/│ ├── active_salbutamol/│ ├── inactive_carazolol/│ └── active_salbutamol_truncated_ICL2/└── README Example File Naming For the MOR/active_DAMGO system:- 1_MOR_active_DAMGO_top.pdb: Topology file for replicate 1- 1_MOR_active_DAMGO_traj.dcd: Trajectory file for replicate 1- 2_MOR_active_DAMGO_top.pdb: Topology file for replicate 2- ... Usage These data files can be used to:- Reproduce the analyses in the manuscript- Perform additional studies based on this data