Dataset of "Molecular basis of the functional conflict between chloroquine and peptide transport in the Malaria parasite chloroquine resistance transporter PfCRT"

This is the source data, set of trajectories, and inputs used to produce them, for the article "Molecular basis of the functional conflict between chloroquine and peptide transport in the Malaria parasite chloroquine resistance transporter PfCRT" (Nature Communications, 2025)

The trajectories contain only the protein and drug molecules (stripped of their water and membrane). This should be sufficient for most follow on analysis, but if it isn't then please feel free to contact one of us, or for any other reason relating to this dataset. 

Please see the paper for the methodological details

Contents and description

minimum_dataset.tar.gz (37.23 GB)

• contains a set of directories each containing the files from a system. The contents of which are specified in the directory name like so:
  • FloodRun_{PfCRT ioform}_{membrange configuration}_{ligand}_{number of ligand molecules in system}_{simulation replicate number}/
• Within each "FloodRun" directory are the files:
  • 'index.ndx' The gromacs format index file specify atom groupings used in the simulation
  • 'mdeq.gro' The full atom post molecular dynamics equilibration structure that was used for the begining of the production runs
  • 'mdeq_Prot-DRUG-only.gro' This file is the same as the above but has the been stripped the same as the trajectory, and so can be used for visualisation of it
  • 'topol-1.tpr' The gromacs 'run file' that generated the production runs. Can be used to directly replicate the simulation there in.
  • 'topol.top'  The topology file used. Note that the forcefield location will be different if you use this for a rerun
  • 'trjcat_centered-Prot_Prot-DRUG-only.xtc' The full strided trajectory file that has had its water and membrane removed. 
• Scripts_and_Paramters/
  • 'create_ndx.py' Creates gromacs index files specific to the system 
  • 'create_top.3.py' Creates gromacs topolgy files specific to the system
  • 'genesis.2.py' Manages the setup of 'FloodRun' directories and systems
  • 'gro_manipulator.py' Performs a number of gromacs structure '.gro' file manipulations for system setup
  • 'insert_molecule.py' Script that handles the insertion of the right number of ligand molecules into the system
  • 'mdeq.mdp' The gromacs parameter file used for the short MD equilibration run
  • 'nore_eq.mdp' The gromacs parameter file used for the short MD equilibration run but without the flat-bottomed harmonic restraint. Used on peptide systems 
  • 'nore_prod.mdp' The gromacs parameter file used for the production run but without the flat-bottomed harmonic restraint. Used on peptide systems 
  • 'prod.mdp' The gromacs parameter file used for the production run
  • 'toppar/ ' The forcefield files used in these simulations

binding_sites.tar.gz (945 KB)

• Contains .pdb files of every binding site determined in the study
  • Systems have been stripped of water and membrane. 
  • For those with multiple binding sites, the final number denotes the rank. 

Source data (57.19  MB)

• Contains the .csv files and .npy files for every graph in the study
• Most files are labelled according to the figure in which they are used. For those that arent:
  • Free-Energy-Surfaces/ contains the .npy file describing the original 3d FES for each isoform-ligand pair. It also contains the FES of resid 76.
  • {isoform}-CQ_binding-site-energies_raw.csv contains all residue binding energies, not just the ones featured in figures 4d and 5d.