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2026
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| Acceso en línea: | https://doi.org/10.5281/zenodo.18468770 |
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| author | Oladele, Tolulope Samuel Iteire, Kingsley Afoke Ogunmiluyi, Oluwafumbi Ebenezer Adebisi, Kayode Adedoyin Siyanbade, Adewale Jacob Sulaiman, Kabirat Adedunmola Leko, Bankole Japhet Ijomone, Omamuyovwi Meashack |
| author_facet | Oladele, Tolulope Samuel Iteire, Kingsley Afoke Ogunmiluyi, Oluwafumbi Ebenezer Adebisi, Kayode Adedoyin Siyanbade, Adewale Jacob Sulaiman, Kabirat Adedunmola Leko, Bankole Japhet Ijomone, Omamuyovwi Meashack |
| contents | <p><strong>Dataset Overview</strong></p> <p>This dataset contains the input and processed molecular dynamics (MD) simulation data supporting the computational findings of our study. The simulations modeled the interaction between the TLR4/MD-2 receptor complex and the lead bioactive ligand β-sesquiphellandrene from <em>Aframomum Melegueta </em>over a 100-nanosecond trajectory.</p> <p>---</p> <p><strong>Associated Project:</strong> <strong>"Integrated In Vivo and In Silico Analysis Reveals <em>Aframomum Melegueta</em> Neuroprotection Against LPS-Induced Memory Impairment Through TLR4/MD-2 Modulation"</strong></p> <p><strong>License:</strong> Creative Commons Attribution 4.0 International (CC-BY 4.0)</p> <p>---</p> <p><strong>File Inventory & Description</strong></p> <ol> <li><strong>Simulation Inputs (Topology & Structure)<br></strong>* complex_solvated.gro`: The final solvated system coordinates (Protein + Ligand + Water + Ions).<br>* topol.top: GROMACS system topology file.<br>* ligand.itp: Ligand topology parameters generated via CGenFF.<br>* index.ndx: Index file defining groups (System, Protein, Ligand, Solvent).<br>* md_input files: .edr, .nvt, .npt, .cpt, .gro files, etc.</li> <li><strong>Production Outputs<br></strong>* md_01 xtc file: Compressed trajectory file (100 ns simulation, frames saved every 10 ps).<br>* md_01 tpr file: The run input file used to generate the trajectory.<br>* md_01 log file: GROMACS log file containing energy and performance data.</li> <li><strong>Analysis Outputs (Processed Data)<br></strong>* rmsd.xvg, rmsf.xvg, potential.xvg, </li> </ol> <p>---</p> <p><strong>Methodology Summary</strong></p> <p>Software: GROMACS (Version 2025.2)<br>Force Field: CHARMM36m (Protein) / CGenFF (Ligand)<br>Water Model: TIP3P<br>Ensemble: NPT (Isothermal-Isobaric)<br>Temperature: 300 K (V-rescale thermostat)<br>Pressure: 1 bar (Parrinello-Rahman barostat)<br>Duration: 100 ns<br>Time Step: 2 fs</p> <p>---</p> <p><strong>Citation</strong></p> <p>If you use this dataset, please cite both the dataset DOI and the associated publication:</p> <p><code><strong>Dataset:</strong> Oladele, T. S., Iteire, K. A., Ogunmiluyi, O. E., Adebisi, K. A., Siyanbade, A. J., Sulaiman, K. A., Leko, B. J., & Ijomone, O. M. (2026). Dataset for Molecular Dynamics Simulation of TLR4/MD-2 Complex with β-Sesquiphellandrene (v1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.18468770</code></p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18468770 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Dataset for Molecular Dynamics Simulation of TLR4/MD-2 Complex with β-Sesquiphellandrene Oladele, Tolulope Samuel Iteire, Kingsley Afoke Ogunmiluyi, Oluwafumbi Ebenezer Adebisi, Kayode Adedoyin Siyanbade, Adewale Jacob Sulaiman, Kabirat Adedunmola Leko, Bankole Japhet Ijomone, Omamuyovwi Meashack Molecular Dynamics Simulation TLR4/MD-2 Aframomum Melegueta β-sesquiphellandrene <p><strong>Dataset Overview</strong></p> <p>This dataset contains the input and processed molecular dynamics (MD) simulation data supporting the computational findings of our study. The simulations modeled the interaction between the TLR4/MD-2 receptor complex and the lead bioactive ligand β-sesquiphellandrene from <em>Aframomum Melegueta </em>over a 100-nanosecond trajectory.</p> <p>---</p> <p><strong>Associated Project:</strong> <strong>"Integrated In Vivo and In Silico Analysis Reveals <em>Aframomum Melegueta</em> Neuroprotection Against LPS-Induced Memory Impairment Through TLR4/MD-2 Modulation"</strong></p> <p><strong>License:</strong> Creative Commons Attribution 4.0 International (CC-BY 4.0)</p> <p>---</p> <p><strong>File Inventory & Description</strong></p> <ol> <li><strong>Simulation Inputs (Topology & Structure)<br></strong>* complex_solvated.gro`: The final solvated system coordinates (Protein + Ligand + Water + Ions).<br>* topol.top: GROMACS system topology file.<br>* ligand.itp: Ligand topology parameters generated via CGenFF.<br>* index.ndx: Index file defining groups (System, Protein, Ligand, Solvent).<br>* md_input files: .edr, .nvt, .npt, .cpt, .gro files, etc.</li> <li><strong>Production Outputs<br></strong>* md_01 xtc file: Compressed trajectory file (100 ns simulation, frames saved every 10 ps).<br>* md_01 tpr file: The run input file used to generate the trajectory.<br>* md_01 log file: GROMACS log file containing energy and performance data.</li> <li><strong>Analysis Outputs (Processed Data)<br></strong>* rmsd.xvg, rmsf.xvg, potential.xvg, </li> </ol> <p>---</p> <p><strong>Methodology Summary</strong></p> <p>Software: GROMACS (Version 2025.2)<br>Force Field: CHARMM36m (Protein) / CGenFF (Ligand)<br>Water Model: TIP3P<br>Ensemble: NPT (Isothermal-Isobaric)<br>Temperature: 300 K (V-rescale thermostat)<br>Pressure: 1 bar (Parrinello-Rahman barostat)<br>Duration: 100 ns<br>Time Step: 2 fs</p> <p>---</p> <p><strong>Citation</strong></p> <p>If you use this dataset, please cite both the dataset DOI and the associated publication:</p> <p><code><strong>Dataset:</strong> Oladele, T. S., Iteire, K. A., Ogunmiluyi, O. E., Adebisi, K. A., Siyanbade, A. J., Sulaiman, K. A., Leko, B. J., & Ijomone, O. M. (2026). Dataset for Molecular Dynamics Simulation of TLR4/MD-2 Complex with β-Sesquiphellandrene (v1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.18468770</code></p> |
| title | Dataset for Molecular Dynamics Simulation of TLR4/MD-2 Complex with β-Sesquiphellandrene |
| topic | Molecular Dynamics Simulation TLR4/MD-2 Aframomum Melegueta β-sesquiphellandrene |
| url | https://doi.org/10.5281/zenodo.18468770 |