Data for Exploring Conformational Landscape of Cryo-EM Using Energy-Aware Pathfinding Algorithm

There are four experiments. The main.ipynb notebook in each experiment directory details the pathfinding process and evaluates different algorithms. Hsp90 (PDB ID: 2CG9): A synthetic dataset with two degrees of conformational changes. The .mrcs and .star files (convert into .pkl file first use cryodrgn functions) serve as training inputs for the cryoDRGN model. NLRP3 (PDB ID: 6NPY): A synthetic dataset with three degrees of conformational changes. The .mrcs and .star files (convert into .pkl file first use cryodrgn functions) serve as training inputs for the cryoDRGN model. EMPIAR-10076 in original latent space. EMPIAR-10076 with Analysis Landscape Pipeline: We also adhere to the analyze landscape pipeline designed by the cryoDRGN team. The Jupyter notebooks in that directory illustrate our implementation of this pipeline for the EMPIAR-10076 dataset, starting with 1_sketching.ipynb and concluding in 2_learning_mapping.ipynb. In the EMPIAR-10076 experiment, we utilize the training weights provided by the official cryoDRGN team. The complete weights and further information can be found here. Additionally, we filter out states unrelated to conformational changes, following the guidance of the labels provided by the cryoDRGN team here.本数据集包含四项实验。各实验目录下的`main.ipynb`脚本详细阐述了路径寻优流程，并对不同算法开展了性能评估。 热休克蛋白90（Hsp90，PDB编号：2CG9）：一款包含两种构象变化程度的合成数据集。其`.mrcs`与`.star`格式文件（需先通过cryoDRGN（cryoDRGN）工具函数转换为`.pkl`格式文件）可作为cryoDRGN模型的训练输入数据。 NLRP3（PDB编号：6NPY）：一款包含三种构象变化程度的合成数据集。其`.mrcs`与`.star`格式文件（需先通过cryoDRGN工具函数转换为`.pkl`格式文件）可作为cryoDRGN模型的训练输入数据。 EMPIAR-10076 原始潜空间（latent space）数据集： 针对EMPIAR-10076的分析景观管线（Analysis Landscape Pipeline）：本研究遵循cryoDRGN团队设计的分析景观管线方案。该目录下的Jupyter笔记本（Jupyter Notebook）展示了我们针对EMPIAR-10076数据集实现的该管线流程，从`1_sketching.ipynb`起始，至`2_learning_mapping.ipynb`收尾。在EMPIAR-10076实验中，我们采用了cryoDRGN官方团队提供的训练权重文件。完整权重文件及更多相关信息可在此处获取。此外，我们参考cryoDRGN团队在此处提供的标注指引，过滤掉了与构象变化无关的样本状态。