A key residue of plant ABC transporter modulates access path geometry and phenylpropanoid substrate selectivity

The input and main output files used for the paper "A key residue of plant ABC transporter modulates access path geometry and phenylpropanoid substrate selectivity" 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)