Directory layout and description for deposited data, scripts, and results associated with Folding correctors can restore CFTR post-translational folding landscape by allosteric domain-domain coupling Naoto Soya, Haijin Xu, Ariel Roldan, Zhengrong Yang, Haoxin Ye, Fan Jiang, Aiswarya Premchandar, Guido Veit, Susan P.C. Cole, John Kappes, Tamas Hegedus, and Gergely L. Lukacs Two files are provided: soya_md_trajectories.tar - This file contains the trajectories merged from the last part (450-500 ns) of the parallel simulations: md_450000_500000.xtc soya_insilico_data.zip - This file contains all other deposited files including input data, scripts, results files. The content of this file can be found below: README.md - the content of this description homo - Homology modeling run*.py, myloopmodel.py, and mymodel.py files are separated for technical reasons, for running model-building in parallel mode cftr-loop - Demonstrates the removal of the RI and seeling the break with loopmodeling mrp1 - Scripts and input files for human MRP1 homology modeling; the large unresolved loop in NBD1 was not modeled but sealed for MD; this required renumbering of the ouput mrp6 - Scripts, input, and output files for human MRP1 homology modeling; output: mrp6_human_closed.pdb; the selected CFTR and MRP1 models were the input for MD simulaitons; to see these energy minimized structures, please see the corresponding 'md' directory below. md - Moldecular dynamics The md_system_info.xlsx file contains the basic properties of simulation boxes MD parameter files: step6*.mdp for minimization and equilibration; step7_production.mdp for production run wordom.dat is the wordom configuration file cmap_mda.mp.py is a script for contact map calculation cftr-*, mrp1-* the simulation system generated by CHARMM-GUI: step5_charmm2gmx.pdb the output gro file of parallel simulations (the last state of the sysmtems): md_[1-6].gro ! the trajectory merged from the last part (450-500 ns) of the parallel simulations: trajectories md_450000_500000.xtc are in a separte file (soya_md_trajectories.tar) with the same directory structure the merged trajectory contains only the SOLU; the corresponding structure file: prot.pdb index.ndx figures figure-3a pdb files are the output of gmx rmsf pse file is saved visualization of the pdb files for PyMOL figure-3c-s4b You can run color_all.tcl in VMD to reproduce the network communities in structural context; this is dependent on the .pdb and .vmd files also deposited in this directory Network community members (residues) are listed in the Word files dri in file names and in scripts refers to 6ss figure-s3a tmd1_structures.pse contains the structures for PyMOL Please see the Source Data file for plotting RMSF Contact map data are in the tmd1_wt.npy and tmd1_r170g.npy file figure-s3e PyMOL pse files to visualise the dynamics of NBD1/2 structures figure-s4a Contains the calculated betweenness.txt files betweenness_plots.py for plotting wt_prot.pdb: required for plotting with resi thick-labels figure-s5c PyMOL pse files to visualise the dynamics of NBD1/2 structures figure-s8d Data for MRP1/ABCC1 You can run color_all.tcl in VMD to reproduce the network communities in structural context; this is dependent on the .pdb and .vmd files also deposited in this directory Network community members (residues) are listed in the Word files