Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions

This data set contains i. input topologies and coordinates for 179 non-modified and post-translationally modified (174 in normal and 87 in stress conditions) yeast protein complexes, ii. scripts and parameters for performing molecular dynamics simulations and binding energy calculation with per-residue decomposition, iii. trajectory snapshots of solvent stripped protein complexes, which can be visualized using the corresponding topology files, iv. RMSD calculations (backbone and entire protein) from the production phase of the MD, and v. pdb of the representative structure of the largest cluster from 100 snapshots of the last 10 ns in each simulation. Additionally, PTMs_map.zip contains a Python script (together with an example) for automated addition of PTMs to protein structures using PyTMs in PyMOL.

本数据集包含以下五部分内容：
i. 179个未修饰及翻译后修饰（PTMs, Post-translational Modifications）酵母蛋白质复合物的输入拓扑结构与坐标信息，其中正常条件下174个，应激条件下87个；
ii. 用于执行分子动力学（MD, Molecular Dynamics）模拟及基于残基分解的结合能计算的脚本与参数；
iii. 经溶剂剥离的蛋白质复合物轨迹快照，可通过对应拓扑文件进行可视化；
iv. 分子动力学模拟生产阶段的主链与全蛋白RMSD（Root Mean Square Deviation，均方根偏差）计算结果；
v. 每次模拟最后10 ns的100个快照中最大聚类的代表性结构的PDB（Protein Data Bank）文件。
此外，PTMs_map.zip压缩包包含一段Python脚本（附带示例），可通过PyMOL中的PyTMs工具实现蛋白质结构上翻译后修饰的自动添加。