Technical Report: Generation of Independent Wild-Type alpha-Synuclein Conformational Ensembles Using All-Atom Molecular Dynamics
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| Natura: | Recurso digital |
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Zenodo
2025
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| _version_ | 1866901893288034304 |
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| author | Functional Dynamics Lab |
| author_facet | Functional Dynamics Lab |
| contents | <p>Alpha-Synuclein is an intrinsically disordered protein (IDP) centrally implicated in Parkinson’s disease pathogenesis. Due to its conformational heterogeneity, single-structure representations are insufficient for mechanistic or therapeutic studies. Here, we report the generation of statistically independent wild-type (WT) alpha-synuclein conformational ensembles using all-atom molecular dynamics (MD) simulations under physiologically relevant conditions. This report documents the complete methodological pipeline, including force field selection, system preparation, equilibration strategy, ensemble independence, and reproducibility controls, providing a transparent and extensible foundation for downstream structural, biophysical, and computational drug discovery analyses. The complete MD code and energy field as well as protein WT and complete ensemble is shared in this repository.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18025728 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Technical Report: Generation of Independent Wild-Type alpha-Synuclein Conformational Ensembles Using All-Atom Molecular Dynamics Functional Dynamics Lab <p>Alpha-Synuclein is an intrinsically disordered protein (IDP) centrally implicated in Parkinson’s disease pathogenesis. Due to its conformational heterogeneity, single-structure representations are insufficient for mechanistic or therapeutic studies. Here, we report the generation of statistically independent wild-type (WT) alpha-synuclein conformational ensembles using all-atom molecular dynamics (MD) simulations under physiologically relevant conditions. This report documents the complete methodological pipeline, including force field selection, system preparation, equilibration strategy, ensemble independence, and reproducibility controls, providing a transparent and extensible foundation for downstream structural, biophysical, and computational drug discovery analyses. The complete MD code and energy field as well as protein WT and complete ensemble is shared in this repository.</p> |
| title | Technical Report: Generation of Independent Wild-Type alpha-Synuclein Conformational Ensembles Using All-Atom Molecular Dynamics |
| url | https://doi.org/10.5281/zenodo.18025728 |