Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters

<p>The input and main output files used for the paper <em><strong>&quot;Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters&quot;</strong></em> are separated in the different tar files depending the MD stage they belong to.</p> <p><strong>Content</strong></p> <p>00_AlphaFold2: The models predicted from AlphaFold2</p> <p>01_build_system: The parameters for ATP and the initial pdb file used to build each system</p> <p>02_minimization: Minimization input files for each variant</p> <p>03_equilibration: Equilibration input files for each variant</p> <p>04_long_equilibration: ATP restrained equilibration input files for each variant</p> <p>05_free_equilibration: Free equilibration input files for each variant</p> <p>06_production: Free production input files for each variant</p> <p>07_caver: Caver calculations for each variant and replica</p> <p>08_transport_tools: Analysis of tunnel networks using TransportTools software</p> <p>09_tunnel_selection: Selection of the tunnels with widest bottleneck radius to perform CaverDock experiments</p> <p>10_caverdock: CaverDock calculations for each variant and for each ligand tested</p> <p>11_membrane_patch: MD simulations for liquiritigenin and POPC membrane only</p> <p>12_MD_analysis: Calculations of RMSD, RMSF of each system. Calculation of helical parameters for trans-membrane helices 2, 5, 8 and 11 (not for APO). Calculation of X1 and X2 angles for residue N1331 in each variant (not for APO)</p> <p>13_US_closed_to_open: Umbrella Sampling simulations to obtain the inward facing (IF) open state of each variant. Not used for PMF analysis.</p> <p>14_US_opening_energy: Umbrella Sampling simulations to obtain the Potential of Mean Force for the transition from IF-closed to IF-open conformations.</p> <p>15_US_equilibration: Equilibration input files for WT and F562L variants in IF-open states.</p> <p>16_US_production: Production input files for WT and F562L variants in IF-open states.</p> <p>17_US_caver: Caver calculations for WT and F562L variants in IF-open states.</p> <p>18_US_transport_tools: Analysis of tunnel networks using TransportTools software of WT and F562L variants in IF-open states.</p> <p>19_US_tunnel_selection: Selection of the tunnels with widest bottleneck radius to perform CaverDock experiments for WT and F562L variants in IF-open states.</p> <p>20_US_caverdock: CaverDock calculations for WT and F562L variants in IF-open states.</p> <p>21_US_MD_analysis: Calculations of RMSD, RMSF of each system. Calculation of helical parameters for trans-membrane helices 2, 5, 8 and 11.</p> <p>ABC_Sequences.fasta: Sequences from 1KP analysis</p>