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license: cc-by-4.0
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# A Dataset of Small Protein Conformational Ensembles from All-Atom Molecular Dynamics Simulations

## Authors
**Zilin Ren**, **Ying Hu**, **Xin Yang**

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## Dataset Overview

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.

## License

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.

## Citing The Dataset

If you use this dataset in your research, please cite the following paper:
[... (Scientific Data, 2026)]  
DOI: https://doi.org/10.57967/HF/7057

## Dataset Structure

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.
  
## Dataset Size

| 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 |