2026-10-14T19:44:15Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33511891 2026-09-16T02:03:56Z category_24655 item_type_3 month_year_09_2026

Molecular dynamics trajectories and analysis data for PPARG and NQO1 in Barrett’s esophagus Jiaying Wu (24755763) Medical biochemistry - proteins and peptides (incl. medical proteomics) Molecular Dynamics trajectories <blockquote><p dir="ltr">This dataset accompanies the manuscript “Integrative transcriptomics and reverse network pharmacology prioritize DPP4 and Achyranthes bidentata in Barrett’s esophagus.”</p><p dir="ltr">It contains molecular dynamics model files, analyzed trajectories, and structural and endpoint-energy results for four complexes: PPARG–rosiglitazone, PPARG–kaempferol, NQO1–dicoumarol, and NQO1–taxifolin. Each complex was simulated in three independently seeded 100 ns production runs, giving twelve trajectories and a total simulation time of 1.2 microseconds.</p><p dir="ltr">S3_Data.zip contains model and topology files, parameter and quality-control records, analysis scripts, structural time series, contact and hydrogen-bond analyses, PPARG helix-12 analyses, NQO1 FAD conformational analyses, and MM-PBSA/MM-GBSA results. Endpoint calculations used 101 snapshots per replica from the fixed 50–100 ns window.</p><p dir="ltr">S4_Data.zip–S9_Data.zip contain the six PPARG trajectories. S10_Data.zip–S21_Data.zip contain the six NQO1 trajectories, each divided into nonoverlapping 0–49.9 ns and 50–100 ns parts. Each coordinate archive includes a trajectory file, reference coordinates, and a README.</p><p dir="ltr">The shared coordinates are analyzed solute trajectories sampled every 100 ps. They retain the protein and ligand, together with both FAD cofactors in the NQO1 systems. They are not the complete solvated production trajectories.</p><p dir="ltr">Reconstruction instructions, software requirements, and file checksums are provided in S3_Data.zip. Preserve the archive filenames when using COORDINATE_MANIFEST.json and reconstruct_coordinates.py. MM-PBSA/MM-GBSA estimates do not include conformational entropy and should not be interpreted as experimental binding free energies.</p></blockquote><p></p> 2026-09-16T02:03:56Z Dataset Dataset 10.6084/m9.figshare.33511891.v1 https://figshare.com/articles/dataset/Molecular_dynamics_trajectories_and_analysis_data_for_PPARG_and_NQO1_in_Barrett_s_esophagus/33511891 CC BY 4.0