Sample trajectories and files required to reproduce the EntDetect Results

compare_sim2exp: Comparison data between simulation and experimental results including cross-linking mass spectrometry (XLMS) consistency analysis and statistical evaluations. EcoliPDBs: Collection of E. coli protein structure files in PDB format, including AlphaFold predicted structures. Foldingpathway_A80%Native: Folding pathway analysis data for trajectories starting from 80% native-like conformations, including Jensen-Shannon divergence metrics. Foldingpathway_random: Folding pathway analysis data for randomly initiated trajectories with metastable state transitions. MSM: Markov State Model analysis files including state mappings, free energy plots, and metastable state distributions for 1ZMR protein dynamics. nativeNCLE: Native state entanglement analysis including Gauss Entanglement (GE) calculations and high-quality entanglement data. nonnative_entanglement_clustering: Clustering analysis of non-native protein entanglements based on topological linking numbers and structural changes. OP_Full: Order parameter calculations using full protein chain topology including Gauss Entanglement values for trajectory analysis. OP_last67_density1: Order parameter calculations focusing on the last 67 residues with specific density settings for entanglement analysis. ReferenceStructures_1ZMR: Reference structure files for 1ZMR protein including cleaned PDB files and topology files (PSF, COR formats). Test_MDtraj: Test trajectory files containing first 100 frames from both all-atom (AA) and coarse-grained (CG) simulations in DCD formatcompare_sim2exp: 模拟与实验结果对比数据集，涵盖交联质谱（cross-linking mass spectrometry, XLMS）一致性分析与统计评估内容。 EcoliPDBs: 大肠杆菌蛋白质结构文件集，采用PDB（Protein Data Bank）格式，包含AlphaFold预测的蛋白质结构。 Foldingpathway_A80%Native: 以80%天然态构象为起始的轨迹折叠通路分析数据集，包含詹森-香农散度（Jensen-Shannon divergence）指标。 Foldingpathway_random: 随机初始轨迹的折叠通路分析数据集，涉及亚稳态转变相关分析。 MSM: 马尔可夫状态模型（Markov State Model, MSM）分析文件集，包含1ZMR蛋白质动力学的状态映射、自由能图及亚稳态分布。 nativeNCLE: 天然态缠结分析数据集，包含高斯缠结（Gauss Entanglement, GE）计算与高质量缠结数据。 nonnative_entanglement_clustering: 基于拓扑连接数与结构变化的非天然蛋白质缠结聚类分析数据集。 OP_Full: 基于完整蛋白质链拓扑的序参数计算数据集，包含轨迹分析所需的高斯缠结数值。 OP_last67_density1: 针对蛋白质最后67个残基的序参数计算数据集，为缠结分析设置了特定密度参数。 ReferenceStructures_1ZMR: 1ZMR蛋白质的参考结构文件集，包含净化后的PDB文件及拓扑文件（PSF、COR格式）。 Test_MDtraj: 测试轨迹文件集，涵盖全原子（all-atom, AA）与粗粒化（coarse-grained, CG）模拟的前100帧数据，格式为DCD。