2026-10-13T22:12:20Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33717490 2026-09-14T10:53:05Z category_24208 item_type_3 month_year_09_2026

Computational reproducibility package for MMP-9 and NLRP3 docking, enrichment, identity, and dynamics audits Bizhi Wei (24867292) Bioinformatics and computational biology not elsewhere classified MMP-9 NLRP3 EGCG molecular docking retrospective enrichment molecular dynamics MM/GBSA reproducibility <p dir="ltr">This dataset and software release supports the manuscript ‘Native-pose recovery, enrichment failure, and ligand-identity sensitivity in MMP-9 and NLRP3 docking.’ It contains frozen receptor-validation records, Vina and Vinardo retrospective benchmark datasets, corrected ligand-identity inputs and docking outputs, processed source tables from three independently seeded 100 ns MMP-9–EGCG molecular-dynamics simulations, audited MM/GBSA outputs, analysis scripts, quality-control records, figure source data and exports, provenance records, and SHA-256 integrity manifests.</p><p><br></p><p dir="ltr">Both Vina and Vinardo recovered the native poses but failed the prespecified retrospective enrichment gate. Corrected EGCG produced a deep-sampling MMP-9 pose consensus but no reproducible NLRP3 pose; the MMP-9 simulations sampled heterogeneous Zn-proximal and alternative pocket states. These outputs support a bounded MMP-9 structural hypothesis and an audited computational workflow. They do not establish biochemical inhibition, direct NLRP3 target engagement, dual-target pharmacology, safety, pharmacokinetics, or therapeutic efficacy.</p><p><br></p><p dir="ltr">The archive includes analysis-ready data and complete file manifests but excludes the full 300 ns raw trajectory segments and bulky engine intermediates; their omission and hashes are documented in EXCLUDED_LARGE_FILES.md and the production audit. Reused public data are from ChEMBL 37 (release 2026-05-01) and RCSB PDB entries 4XCT and 9GU4 and remain subject to their original source terms. No human-participant, clinical, or wet-laboratory data were generated.</p> 2026-09-14T10:53:05Z Dataset Dataset 10.6084/m9.figshare.33717490.v1 https://figshare.com/articles/dataset/Computational_reproducibility_package_for_MMP-9_and_NLRP3_docking_enrichment_identity_and_dynamics_audits/33717490 CC BY 4.0