Dataset for "Optimal Enhanced Sampling of Protein Conformational Changes by Extract Reaction Coordinates from Energy Relaxation"

This set of files contain the data generated in the paper titled: Optimal Enhanced Sampling of Protein Conformational Changes by Extract Reaction Coordinates from Energy Relaxation. The RC-uncovered trajectories along the leading SCs of HIV protease and PDZ2 domain are available here. Also listed are the natural trajectories for ligand dissociation in HIV protease and PDZ2 domain that correspond to supplementary videos S3, S4 and S5. In each case, .xtc files are trajectory files in GROMACS format, the .py file is the corresponding UCSF Chimera file and the .cxs file is the corresponding ChimeraX file. ChimeraX is the latest upgrade of Chimera. In each Chimera or ChimeraX file, the structure in white color is a equilibrated structure from MD simulation, which is used as reference for comparison.

本数据集收录了题为《通过从能量弛豫中提取反应坐标（Reaction Coordinate, RC）》的论文所生成的全部实验数据。本数据集提供了HIV蛋白酶（HIV protease）与PDZ2结构域（PDZ2 domain）沿主导慢集体坐标（Slowest Collective Coordinates, SCs）分布的未提取反应坐标轨迹。此外还列出了对应补充视频S3、S4、S5的HIV蛋白酶与PDZ2结构域配体解离过程的天然轨迹。各类文件格式说明如下：.xtc文件为GROMACS格式的轨迹文件；.py文件为适配UCSF Chimera的脚本文件；.cxs文件为适配ChimeraX的脚本文件。其中，ChimeraX是Chimera的最新升级版本。在每个Chimera或ChimeraX文件中，以白色呈现的结构为分子动力学（Molecular Dynamics, MD）模拟得到的平衡态结构，用作比对参照。