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| # A Dataset of Small Protein Conformational Ensembles from All-Atom Molecular Dynamics Simulations |
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| ## Authors |
| **Zilin Ren**, **Ying Hu**, **Xin Yang** |
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| ## Dataset Overview |
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| This dataset, hereafter referred to as **DynoDB**, consists of 8,385 molecular dynamics (MD) trajectories of small proteins (5–100 amino acids). Each entry contains 1,000 ensemble frames extracted from 100 ns production runs, providing a systematic characterization of small protein conformational landscapes at the atomic scale. |
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| ## License |
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| This dataset is licensed under the **Creative Commons Attribution 4.0 International License (CC BY 4.0)**. By using this dataset, you agree to cite the original work as specified below. |
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| ## Citing The Dataset |
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| If you use this dataset in your research, please cite the following paper: |
| [... (Scientific Data, 2026)] |
| DOI: https://doi.org/10.57967/HF/7057 |
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| ## Dataset Structure |
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| The data is organized as follows: |
| - `static_structures/`: Initial PDB conformations. |
| - `processed_structures/`: Preprocessed and repaired models. |
| - `trajectory_frames/`: Extracted frames (1,000 per system). |
| - `metadata/`: Multi-sheet Excel/CSV files providing comprehensive structural, dynamic, and functional annotations. |
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| ## Dataset Size |
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| | Dataset Metric | Value | |
| | :--- | :--- | |
| | Number of trajectories | 8,385 | |
| | Length per trajectory | 100 ns | |
| | Cumulative simulation time | 838.5 µs (~0.84 s) | |
| | Total number of atoms | 3,990,516 | |
| | Average system size (atoms) | ~476 | |
| | Total number of residues | 491,395 | |
| | Average system size (residues) | ~59 | |
| | Storage size | ~611 GB | |
