Datasets for the reproduction of Ensemble-Driven Molecular Dynamics (EDMD) structure refinement

The repository consists of folders for different proteins, serving as examples.The prefixes refers to the origin of the dataset:Abrelax: data from CS-Rosetta Abinitio Relax protocol.NOE-RASREC: data from CS-Rosetta RASREC protocol supplemented with NOE-derived distance restraints.Every protein folder includes the following:"ExtractedPDBs" folder storing the individual PDB files of the structural ensemble (from CS-Rosetta structure prediction) and "name.scores.txt" file with filenames and belonging scores."results_trajectories" folder with XTC trajectory files from GROMACS. EDMD trajectories were calculated with the force field modified with the EDMD package. MD trajectories were run with the original AMBER force field. 2-2 parallel 1000 ns long simulations are presented."_grompp.tpr" file, from which it is possible to run EDMD simulations."_processed.top" file is a processed topology file."_solv_ions.gro" file is a GRO file ready to run simulations. It contains the solvated protein (best model of the ensemble).NDX index file."EDMD_config.json" is a configuration file to run the EDMD package.Details about the EDMD package can be found at https://github.com/gadaneczm/EDMD_package.Publication: https://doi.org/10.1021/acs.jcim.5c02358.