Computational data for peptide SPAFESTWDILK/target MDM2: molecular dynamics trajectories, AF3 benchmark, multi-method binding evaluation

README — SPAFESTWDILK / MDM2 computational data deposit Supporting data for the SPAFESTWDILK / MDM2 manuscript (Sherman Tree Nutraceuticals, in preparation). Letter codes in brackets correspond to the data references [a]–[z] in the manuscript Section 6 (Data and Code Availability). Files marked "Zenodo" are included in this deposit. Items marked "external" are hosted on Neurosnap, GitHub or ExPASy and are listed here for completeness with the link given in the manuscript. DATA REFERENCES [a] Pipeline notebook (PepVeg) — GitHub: https://github.com/Kingelanci/PepVeg-Pipeline peptides_hydrolysis.zip — Step 1 hydrolysis library, 8,645,509 unique fragments. (Zenodo) [b] ESM-2 top 2000 JSON — esm2_top2000_MDM2.json. (Zenodo) [c] Pharmacophore candidates — export_MDM2_fitoterapici.zip. (Zenodo) [d] AF3 Server controls (raw JSON) — AF3_8_calibration_peptides.zip. 3+3 calibration panel and SPAFESTWDILK runs, 8 peptides x 5 seeds (manifest.tsv included inside). (Zenodo) [e] AF3 expanded benchmark (raw JSON) — AF3_29_hard_negatives.zip. 29 hard-negative peptides x 5 seeds. (Zenodo) [f] Protenix SPAFESTWDILK — Protenix_structure_predictions.zip. 5 models. (Zenodo) External: https://neurosnap.ai/job/69df686cc7a74174eaf1a524?share=69e22150eec1918b946621fe [g] Chai-1 SPAFESTWDILK — Chai-1_structure_predictions.zip. 5 models. (Zenodo) External: https://neurosnap.ai/job/69df6680c7a74174eaf1a51c?share=69e22150eec1918b9466220e [h] EvoEF2 Protenix structure — EvoEF2_Protenix_structure.zip. -55.57 EEU (manuscript reference value). (Zenodo) External: https://neurosnap.ai/job/69df74bfc7a74174eaf1a585?share=69e22151eec1918b94662212 [i] EvoEF2 AF3 structure — EvoEF2_AF3_structure.json. -47.27 EEU. (Zenodo) [j] GROMACS AMBER 50ns Protenix — external only. https://neurosnap.ai/job/69df8c8dc7a74174eaf1a6d5?share=69e22151eec1918b94662216 [k] GROMACS AMBER 50ns AF3 — external only. https://neurosnap.ai/job/69e0bca1c7a74174eaf1b631?share=69e22151eec1918b9466221a [l] GROMACS CHARMM27 50ns — external only. https://neurosnap.ai/job/69e0f5b3c7a74174eaf1b9d9?share=69e22151eec1918b9466221c [m] GROMACS p53(17-29) control 50ns — external only. https://neurosnap.ai/job/69e12b80c7a74174eaf1bc65?share=69e22151eec1918b9466221e [n] GROMACS xvg raw data — GROMACS_xvg_110files.zip. 110 .xvg files from the CHARMM36m simulations: 5 ns triage of 16 systems plus 100 ns production runs of the three promoted candidates (SPAFESTWDILK, EFSDLWDNK, FQSWEDLSK). Poly-Ala and DDFLNSWK lack the gyrate/hbond outputs (no stable complex to analyse). (Zenodo) [o] MM-PBSA AMBER — MMPBSA_AMBER_50ns.zip. gmx_MMPBSA on AMBER99SB-ILDN trajectory, dG = -75.30 +/- 4.92 kcal/mol. (Zenodo) External: https://neurosnap.ai/job/69dfc05fc7a74174eaf1a983?share=69e22152eec1918b94662222 [p] MM-PBSA CHARMM27 — MMPBSA_CHARMM27_50ns.zip. gmx_MMPBSA on CHARMM27 trajectory, dG = -55.07 +/- 2.86 kcal/mol. (Zenodo) External: https://neurosnap.ai/job/69e12743c7a74174eaf1bc52?share=69e22152eec1918b94662224 [q] Protenix PMI — external only. https://neurosnap.ai/job/69df89d5c7a74174eaf1a688?share=69e22150eec1918b94662202 [r] Protenix p53(15-29) — external only. https://neurosnap.ai/job/69df89bbc7a74174eaf1a686?share=69e22150eec1918b94662204 [s] Protenix poly-Ala — external only. https://neurosnap.ai/job/69df8844c7a74174eaf1a678?share=69e22150eec1918b94662206 [t] Protenix W23A — external only. https://neurosnap.ai/job/69df89f1c7a74174eaf1a68a?share=69e22150eec1918b94662208 [u] Protenix W8A — external only. https://neurosnap.ai/job/69df8956c7a74174eaf1a682?share=69e22150eec1918b9466220a [v] Protenix scrambled — external only. https://neurosnap.ai/job/69df88acc7a74174eaf1a67f?share=69e22150eec1918b9466220c [w] GROMACS SVG figures — GROMACS_31_SVG.zip. 31 vector SVG figures of the GROMACS analyses. (Zenodo) [x] PyMOL scripts — PyMOL_Scripts_Structural_Figures.docx. Scripts for Figure 4, Figure S4, Figure S7. (Zenodo) [y] PDB structures and GROMACS input files — 5NS.rar and 100ns.rar. (Zenodo) 5NS.rar — 17 systems, 5 ns CHARMM36m triage: Plant-derived candidates (F-x(1-3)-W pharmacophore): SPAFESTWDILK Zingiber officinale (ginger) [LEAD] FESTWDILK Zingiber officinale (ginger) HAFPELWNIEK Zingiber officinale (ginger) DDFLNSWK Camellia sinensis (green tea) EFSDLWDNK Vanilla planifolia (vanilla) DNEFLQDWSK Artemisia SDLTSFMEEWR Artemisia FQSWEDLSK Cordyceps QNSFVDLWK Grifola frondosa (maitake) ISTAFLNDWDLAK Grifola frondosa (maitake) EHFETLWSSVK plant proteome candidate Hard negatives: EWSLDQSKF Cordyceps (scrambled) FSNLDKWDE Vanilla (scrambled) WSADITKFESPL Zingiber officinale (scrambled) FWELDSTLKLPNEQS scrambled Reference negative controls: AAAAAAAAAAAAAAAAA poly-Ala 17-mer SQETFSDLAKLLPEN p53(15-29) W23A mutant 100ns.rar — 100 ns CHARMM36m production runs of the three promoted candidates: SPAFESTWDILK, EFSDLWDNK, FQSWEDLSK. Each archive contains: .pdb, .top/.itp, .mdp, .xtc, .tpr, .gro and .xvg analysis outputs. [z] ExPASy ProtParam — external only. https://web.expasy.org/protparam/ (sequence SPAFESTWDILK) ADDITIONAL FILES IN THIS DEPOSIT (not letter-coded but cited in the manuscript)26_NutrAI_candidates.csv — 26 pharmacophore-passing candidates submitted to AF3.benchmark_3+3_panel.csv — 3+3 AF3 calibration panel. License: CC BY 4.0