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. <strong>README.txt </strong>- instruction for script usage 2. <strong>PDBs.zip</strong> - PDB structures of complexes in water box used in the analysis, ligand PDB and mol2 structures 3. <strong>tauRAMD_v2.py </strong>- Python sctipt for estimation relative residence times from Gromacs-RAMD output 4. <strong>IFP_preprocess_Gromacs.py</strong> and <strong>IFP_SL-B2AR-WB-EX.py - </strong>Python scripts for preprocessing of RAMD trajectories and generation of IFPs 5. <strong>Scripts.zip</strong> - additional python functions 6. <strong>IXO-CHL.zip, IXO-ALO-CHL.zip, ACh-CHL.zip, b2AR.zip</strong> - Protein-Ligand Interaction Fingerprints (PL IFPs) generated from RAMD trajectories for <em>mAChR M2 with iperoxo</em>, <em>mAChR M2 </em><em> with iperoxo and PAM, mAChR M2 with ACh, and </em>β<em>2AR with alprenolol </em><em>.</em> 7. <strong>Topology.zip</strong> - Gromacs topology, index.ndx, and coordinate gro files for all four systems 8. <strong>Example_b2AR-alprenolol.zip </strong>- a set of data for a test example showing how IFP can be generated from RAMD trajectories (including several representative trajectories) 9. <strong>Example_b2AR-alprenolol.tar </strong>- 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.<strong> Gromacs-IFP-GPCR.ipynb</strong> - Jupyter Notebook for analysis of trajectories using generated IFP data 11. <strong>Auxi-Plots-GPCR.ipynb - </strong>Jupyter Notebook for generation additional plots from the paper 12. <strong>Waters.zip</strong> - number of water molecules in the binding pocket in dissociation trajectories of the <em> </em>β<em>2AR - alprenolol system</em> 13. <strong>GPCR.yml</strong> - JN environment file