Molecular Dynamics Dataset of Ecdysone Receptor Reveals Allosteric Modulation by Azadirachtin and Eugenol
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| Format: | Recurso digital |
| Sprache: | Englisch |
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2026
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| _version_ | 1866902014650220544 |
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| author | Nalgirkar, Harsh Choure, Rajendra |
| author_facet | Nalgirkar, Harsh Choure, Rajendra |
| contents | <p>This dataset contains molecular dynamics simulations and analysis of the Ecdysone Receptor (EcR) in four systems: APO, AZA-bound, EUG-bound, and dual-ligand (AZA+EUG).</p> <p>The dataset includes:<br>- CHARMM-GUI generated simulation inputs<br>- Curated MD trajectories (200 ns)<br>- Structural and dynamical analyses (RMSD, RMSF, SASA, Rg, PCA, FEL, DCCM)<br>- Cryptic pocket analysis<br>- Reproducible analysis scripts</p> <p>The data supports mechanistic insights into ligand cooperativity and allosteric modulation in EcR.</p> <p>Folder structure:<br>1_input_structures → initial PDB and docking files <br>2_simulation_parameters → simulation inputs and topology <br>3_trajectories → curated MD trajectories <br>4_analysis → all analysis outputs <br>5_scripts → reproducible scripts <br>6_figures_publication → final figures <br>7_supplementary → additional data </p> <p>All simulations were performed using GROMACS with CHARMM36 force field.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_19491919 |
| institution | Zenodo |
| language | eng |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Molecular Dynamics Dataset of Ecdysone Receptor Reveals Allosteric Modulation by Azadirachtin and Eugenol Nalgirkar, Harsh Choure, Rajendra Molecular Dynamics, Allostery, Ecdysone Receptor, GROMACS, PCA, DCCM, Protein Dynamics <p>This dataset contains molecular dynamics simulations and analysis of the Ecdysone Receptor (EcR) in four systems: APO, AZA-bound, EUG-bound, and dual-ligand (AZA+EUG).</p> <p>The dataset includes:<br>- CHARMM-GUI generated simulation inputs<br>- Curated MD trajectories (200 ns)<br>- Structural and dynamical analyses (RMSD, RMSF, SASA, Rg, PCA, FEL, DCCM)<br>- Cryptic pocket analysis<br>- Reproducible analysis scripts</p> <p>The data supports mechanistic insights into ligand cooperativity and allosteric modulation in EcR.</p> <p>Folder structure:<br>1_input_structures → initial PDB and docking files <br>2_simulation_parameters → simulation inputs and topology <br>3_trajectories → curated MD trajectories <br>4_analysis → all analysis outputs <br>5_scripts → reproducible scripts <br>6_figures_publication → final figures <br>7_supplementary → additional data </p> <p>All simulations were performed using GROMACS with CHARMM36 force field.</p> |
| title | Molecular Dynamics Dataset of Ecdysone Receptor Reveals Allosteric Modulation by Azadirachtin and Eugenol |
| topic | Molecular Dynamics, Allostery, Ecdysone Receptor, GROMACS, PCA, DCCM, Protein Dynamics |
| url | https://doi.org/10.5281/zenodo.19491919 |