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.本仓库包含针对各类蛋白质的示例文件夹，文件夹前缀代表数据集来源： - Abrelax：数据源自CS-Rosetta Abinitio Relax协议； - NOE-RASREC：数据源自CS-Rosetta RASREC协议，并补充了基于NOE（核Overhauser效应）推导的距离约束。 每个蛋白质文件夹均包含以下内容： 1. ExtractedPDBs文件夹：存储结构集合的单条PDB文件（源自CS-Rosetta结构预测结果），以及`name.scores.txt`文件，该文件记录了文件名与对应的评分； 2. results_trajectories文件夹：包含来自GROMACS的XTC轨迹文件。其中，EDMD轨迹通过经EDMD工具包修改后的力场计算得到；MD轨迹则使用原始AMBER力场运行，共包含2组并行的1000 ns时长模拟； 3. `_grompp.tpr`文件：可用于启动EDMD模拟； 4. `_processed.top`文件：为处理后的拓扑文件； 5. `_solv_ions.gro`文件：为可直接启动模拟的GRO文件，其中包含溶剂化后的蛋白质（即结构集合中的最优模型）； 6. NDX索引文件； 7. `EDMD_config.json`：用于运行EDMD工具包的配置文件。 有关EDMD工具包的详细信息，请访问：https://github.com/gadaneczm/EDMD_package。 相关发表文献：https://doi.org/10.1021/acs.jcim.5c02358。