G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tauRAMD Simulations

Data  and Python scripts used for generation and analysis of RAMD  dissociation trajectories for several GPCR complexes (including example showing generation of  the Protein-Ligand Interaction Fingerprints, IFP, for several representative RAMD trajectories),

reported in the manuscript

"G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tRAMD Simulations" "G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tauRAMD Simulations"

by Daria B. Kokh, Rebecca C. Wade

submitted to  the Journal of Chemical Theory and Computation

1. README.txt - instruction for script usage

2. PDBs.zip - PDB structures of complexes in water box used in the analysis, ligand PDB and mol2 structures

3. tauRAMD_v2.py - Python sctipt for estimation relative residence times from Gromacs-RAMD output 

4. IFP_preprocess_Gromacs.py and IFP_SL-B2AR-WB-EX.py - Python scripts for preprocessing of RAMD trajectories and generation of IFPs

5. Scripts.zip - additional python functions 

6. IXO-CHL.zip, IXO-ALO-CHL.zip, ACh-CHL.zip, b2AR.zip - Protein-Ligand Interaction Fingerprints (PL IFPs) generated from RAMD trajectories  for mAChR M2 with iperoxo, mAChR M2 with iperoxo and  PAM, mAChR M2 with ACh, and  β2AR with alprenolol .  

7. Topology.zip - Gromacs topology, index.ndx, and coordinate gro files for  all four systems

8. Example_b2AR-alprenolol.zip - a set of data for a test example showing how IFP can be generated from RAMD trajectories (including several representative trajectories)

9. Example_b2AR-alprenolol.tar - almost  the same set of data as above  (compressed in Windows) but for Linux users. The only difference between tar and zip archive: a short equilibration trajectory that is missing in the zip set but is  included in the tar archive.

10. Gromacs-IFP-GPCR.ipynb - Jupyter Notebook for analysis of trajectories using generated IFP data

11. Auxi-Plots-GPCR.ipynb - Jupyter Notebook for generation additional plots from the paper

12. Waters.zip - number of water molecules in the binding pocket in dissociation trajectories of the  β2AR - alprenolol system

13. GPCR.yml - JN environment file