Sample trajectories and files required to reproduce the EntDetect Results
收藏Zenodo2026-01-13 更新2026-05-26 收录
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https://zenodo.org/doi/10.5281/zenodo.18232474
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资源简介：
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
提供机构：
Zenodo
创建时间：
2026-01-13
