Raw MD data for "Metastable Protein−Protein Interactions as a Design Principle for PROTACs: Insights from the RIPK1−VHL System"

MD Simulation data for the Publication “Metastable Protein−Protein Interactions as a Design Principle for PROTACs: Insights from the RIPK1−VHL System” (JACS Au)

Raw_Trajs.tar.gz: raw simulation data (~420 μs) for the sampling of the linker-free RIPK1-VHL encounter complexes. Given the size limit, only solute trajectories are included, and the saving interval is 1 ns. For generating these data, we offer special thanks to Folding@Home platform (https://foldingathome.org/).

Docking_Trajs.tar.gz: raw simulation data for the sampling of the ternary complexes after docking by DiffDock. Inside, there are four folders, including ./Site2_Linker_State3, ./Site2_Linker_State5, ./Site3_Linker_State3, and ./Site3_Linker_State4. For each compatible PROTAC-PPI pair, all the 5 simulation trajectories are provided.

本数据集为发表于《JACS Au》期刊的论文《亚稳态蛋白质-蛋白质相互作用作为蛋白降解靶向嵌合体(Proteolysis Targeting Chimeras, PROTACs)的设计原则：来自受体相互作用蛋白激酶1(Receptor-interacting protein kinase 1, RIPK1)−希佩尔-林道蛋白(Von Hippel-Lindau, VHL)系统的启示》的配套分子动力学(Molecular Dynamics, MD)模拟数据。

Raw_Trajs.tar.gz：用于采样无连接子的RIPK1-VHL偶遇复合物的原始模拟数据（约420微秒）。受文件大小限制，仅包含溶质轨迹，保存间隔为1纳秒。本数据集的生成特别致谢Folding@Home平台（https://foldingathome.org/）的支持。

Docking_Trajs.tar.gz：经DiffDock对接后的三元复合物采样原始模拟数据。该压缩包内包含四个文件夹，分别为./Site2_Linker_State3、./Site2_Linker_State5、./Site3_Linker_State3及./Site3_Linker_State4。针对每一组兼容的蛋白降解靶向嵌合体-蛋白质相互作用(Proteolysis Targeting Chimeras-Protein-Protein Interaction, PROTAC-PPI)对，均提供全部5条模拟轨迹。