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

<p>Data&nbsp; and Python scripts&nbsp;used for generation and analysis of&nbsp;RAMD&nbsp; dissociation trajectories for&nbsp;several GPCR complexes (including example showing generation of&nbsp; the Protein-Ligand Interaction Fingerprints, IFP, for several representative RAMD trajectories),</p> <p>reported in the manuscript</p> <p>&quot;G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tRAMD Simulations&quot;&nbsp;&quot;G-Protein Coupled Receptor-Ligand Dissociation Rates and Mechanisms from tauRAMD Simulations&quot;</p> <p>by&nbsp;Daria B. Kokh, Rebecca C. Wade</p> <p>submitted to&nbsp; the Journal of Chemical Theory and&nbsp;Computation</p> <p>&nbsp;</p> <p>1. <strong>README.txt </strong>- instruction for script usage</p> <p>2. <strong>PDBs.zip</strong> - PDB structures of complexes in water box used in the analysis, ligand PDB and mol2 structures</p> <p>3. <strong>tauRAMD_v2.py </strong>- Python sctipt&nbsp;for&nbsp;estimation relative residence times from Gromacs-RAMD&nbsp;output&nbsp;</p> <p>4.&nbsp;<strong>IFP_preprocess_Gromacs.py</strong> and&nbsp;<strong>IFP_SL-B2AR-WB-EX.py - </strong>Python scripts for preprocessing of RAMD trajectories and generation of IFPs</p> <p>5. <strong>Scripts.zip</strong> - additional python functions&nbsp;</p> <p>6.&nbsp;<strong>IXO-CHL.zip, IXO-ALO-CHL.zip, ACh-CHL.zip, b2AR.zip</strong> - Protein-Ligand Interaction Fingerprints (PL IFPs)&nbsp;generated from RAMD trajectories&nbsp; for&nbsp;<em>mAChR M2 with iperoxo</em>,&nbsp;<em>mAChR M2 </em><em> with iperoxo and&nbsp; PAM, mAChR M2 with ACh, and&nbsp;&nbsp;</em>&beta;<em>2AR with&nbsp;alprenolol </em><em>.</em>&nbsp;&nbsp;</p> <p>7. <strong>Topology.zip</strong> - Gromacs topology, index.ndx, and coordinate gro files for&nbsp; all four systems</p> <p>8.&nbsp;<strong>Example_b2AR-alprenolol.zip&nbsp;</strong>- a set of data for a test example&nbsp;showing how IFP can be generated from RAMD trajectories (including several representative trajectories)</p> <p>9.&nbsp;<strong>Example_b2AR-alprenolol.tar&nbsp;</strong>- almost&nbsp; the same set of data as above&nbsp; (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&nbsp; included in the tar archive.</p> <p>10.<strong>&nbsp;Gromacs-IFP-GPCR.ipynb</strong> - Jupyter Notebook for analysis of trajectories using generated IFP data</p> <p>11. <strong>Auxi-Plots-GPCR.ipynb -&nbsp;</strong>Jupyter Notebook for generation additional plots from the paper</p> <p>12. <strong>Waters.zip</strong> -&nbsp;number of&nbsp;water molecules in the binding pocket in&nbsp;dissociation trajectories of the&nbsp;<em>&nbsp;</em>&beta;<em>2AR -&nbsp;alprenolol system</em></p> <p>13. <strong>GPCR.yml</strong> - JN environment file</p> <p>&nbsp;</p>