DISTIL: Derived Analysis Results and Simulation Reproducibility Materials

This record provides derived analysis results and simulation-reproducibility materials supporting the study: “DISTIL: Distribution-Aware Detection and Interpretation of Structural Differences in Molecular Dynamics Ensembles” DISTIL is an alignment-free method for comparing molecular-dynamics structural ensembles using empirical distributions of internal atom-pair and residue-pair distances and for reconstructing detected differences as ranked relationships between structural regions. The record contains two archives: 1. `DISTIL_Zenodo_results.zip` Derived DISTIL analysis materials, including analysis settings, feature-level metrics, selected-feature tables, feature-correlation data, bundle and structural-region-pair results, feature-contribution data, numerical source data underlying the reported representative-distance distributions, reference and visualization structures, execution provenance, file manifests, and SHA256 checksums. 2. `DISTIL_simulation_reproducibility.zip` Redistributable simulation-setup materials, including initial and reference structures, prepared coordinate files, topology and parameter files, SHAKE-constraint files, water-boundary definitions, j_presto input files, batch-set inputs, preparation commands, molecular-dynamics command files, explanatory README files, a file manifest, and SHA256 checksums. Raw molecular-dynamics trajectories for T4 lysozyme and PDZ2 are not included because of their large data volume. They are available from the corresponding author upon reasonable request. The CYP102A1/BM3–(S)-(-)-limonene and poly-lysine trajectories were generated in previously published studies and are not redistributed in this record. The DISTIL implementation used in the study is publicly available as part of j_presto: https://github.com/jikebe-AIST/j_presto License note: The stated record license applies to original data, documentation, and materials created for this deposit. Any identifiable third-party source materials remain subject to the terms of their original providers. The j_presto software is distributed separately under the license specified in its GitHub repository.