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

The input and main output files used for the paper "Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters" are separated in the different tar files depending the MD stage they belong to.

Content

00_AlphaFold2: The models predicted from AlphaFold2

01_build_system: The parameters for ATP and the initial pdb file used to build each system

02_minimization: Minimization input files for each variant

03_equilibration: Equilibration input files for each variant

04_long_equilibration: ATP restrained equilibration input files for each variant

05_free_equilibration: Free equilibration input files for each variant

06_production: Free production input files for each variant

07_caver: Caver calculations for each variant and replica

08_transport_tools: Analysis of tunnel networks using TransportTools software

09_tunnel_selection: Selection of the tunnels with widest bottleneck radius to perform CaverDock experiments

10_caverdock: CaverDock calculations for each variant and for each ligand tested

11_membrane_patch: MD simulations for liquiritigenin and POPC membrane only

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)

13_US_closed_to_open: Umbrella Sampling simulations to obtain the inward facing (IF) open state of each variant. Not used for PMF analysis.

14_US_opening_energy: Umbrella Sampling simulations to obtain the Potential of Mean Force for the transition from IF-closed to IF-open conformations.

15_US_equilibration: Equilibration input files for WT and F562L variants in IF-open states.

16_US_production: Production input files for WT and F562L variants in IF-open states.

17_US_caver: Caver calculations for WT and F562L variants in IF-open states.

18_US_transport_tools: Analysis of tunnel networks using TransportTools software of WT and F562L variants in IF-open states.

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.

20_US_caverdock: CaverDock calculations for WT and F562L variants in IF-open states.

21_US_MD_analysis: Calculations of RMSD, RMSF of each system. Calculation of helical parameters for trans-membrane helices 2, 5, 8 and 11.

ABC_Sequences.fasta: Sequences from 1KP analysis