AA-MD simulation beta-sitosterol (BST), sonidegib (SNG) and cholesterol (CLR) with smoothened protein (SMO)

The data provided here are the raw and supplementary data for all atom (AA) molecular dynamic simulations of beta-sitosterol, sonidegib and cholesterol with smoothened protein (SMO), respectively. There are three folder; SMO-BST, SMO-CLR and SMO-SNG. In each folder, the topology (.tpr) and trajectory (.xtc) of respected complex for 10 ns of MD simulation were embedded together with four sub-folders of raw data from GROMACS package simulation, PyContact, g_mmpbsa and distance analysis. The distance folder contains the index file for targeted residues and also the video (.mpg and .mp4 format) of distance simulation between ARG451 and TRP535 residues produced by VMD software and online conversion tool. The GROMACS folder contains important execution files for smoothened and ligand topology preparation, solvation, energy minimization, equilibration, and molecular dynamic productions. The g_mmpbsa folder contains the output files (.dat) from the calculation of energy component. This folder also comprises of the PDB files containing energy values in B-factor which can be visualized by VMD software. The PyContact folder having the original outputs (.png) of interaction analysis between SMO and ligand that were generated from PyContact tool. The .tpr and .xtc files from MD production using GROMACS are important for the generation of raw data in g_mmpbsa, PyContact and distance analysis.

本次提供的数据为β-谷甾醇(beta-sitosterol)、索尼德吉(sonidegib)与胆固醇(cholesterol)分别与smoothened蛋白(SMO)开展全原子(AA)分子动力学模拟的原始数据与补充数据。本数据集共包含三个文件夹，分别为SMO-BST、SMO-CLR与SMO-SNG。每个文件夹内均存储了对应复合物10 ns分子动力学模拟的拓扑文件(.tpr)与轨迹文件(.xtc)，同时附带四个子文件夹，分别存放来自GROMACS软件包模拟、PyContact、g_mmpbsa及距离分析的原始数据。其中，距离分析子文件夹内含目标残基的索引文件，同时包含由VMD软件及在线转换工具生成的ARG451与TRP535残基间距离模拟视频，格式为.mpg与.mp4。GROMACS子文件夹内含smoothened蛋白与配体拓扑结构制备、溶剂化、能量最小化、平衡化及分子动力学生产模拟所需的关键执行文件。g_mmpbsa子文件夹包含能量组分计算得到的输出文件（格式为.dat），同时还包含以B因子形式存储能量值的PDB文件，可通过VMD软件进行可视化展示。PyContact子文件夹内含由PyContact工具生成的SMO与配体间相互作用分析的原始输出结果，格式为.png。通过GROMACS完成分子动力学生产模拟得到的.tpr与.xtc文件，是生成g_mmpbsa、PyContact及距离分析所需原始数据的关键文件。