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 format