Evolutionary constraints preserve dynamic interaction networks that enable high-temperature adaptation in thermophilic β-glucosidases

Evolutionary constraints preserve dynamic interaction networks that enable high-temperature adaptation in thermophilic β-glucosidases Data Section The raw data were derived from β-glucosidase-related datasets and stored in the ./data folder. The training and test datasets are deposited in the NRI folder. Molecular Dynamics (MD) Simulation Section Files pertaining to interpretability analysis are stored in the MD_datas folder, including the corresponding initial PDB files, XTC trajectory files, as well as datasets of Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Secondary Structure Content (SSC). Scripts such as jiechu.py and rmsd-q-300bs2.py in the MD folder are utilized for trajectory visualization and quantitative analysis of MD simulations. Model Section The initial PDB files, filtered output matrix files, and script file (trst.ipynb) for constructing the Neural Relational Inference (NRI) model are stored in the NRI folder. Evolution Section The structural sequences associated with family co-evolution, together with the generation and processing files of model language parameters, are all deposited in the Evolution folder.进化约束维系嗜热β-葡萄糖苷酶中赋予高温适应性的动态相互作用网络 数据板块 原始数据来源于β-葡萄糖苷酶相关的数据集，存储于./data文件夹中。训练集与测试集存放于NRI文件夹内。 分子动力学（Molecular Dynamics，MD）模拟板块 与可解释性分析相关的文件存储于MD_datas文件夹中，包括对应的初始PDB文件、XTC轨迹文件，以及均方根偏差（Root Mean Square Deviation，RMSD）、均方根波动（Root Mean Square Fluctuation，RMSF）和二级结构含量（Secondary Structure Content，SSC）数据集。MD文件夹内的jiechu.py、rmsd-q-300bs2.py等脚本可用于轨迹可视化与分子动力学模拟的定量分析。 模型板块 用于构建神经关系推理（Neural Relational Inference，NRI）模型的初始PDB文件、经过滤的输出矩阵文件以及脚本文件（trst.ipynb）均存储于NRI文件夹中。 进化分析板块 与家族共进化相关的结构序列，以及模型语言参数的生成与处理文件，均存放于Evolution文件夹内。