Update README.md

README.md

@@ -1,29 +1,40 @@
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-license: gpl-3.0
+license: cc-by-4.0
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-# DynoDB: a database of small protein conformational ensembles from all-atom molecular dynamics simulations
+# A Dataset of Small Protein Conformational Ensembles from All-Atom Molecular Dynamics Simulations
 
-<!-- Provide a quick summary of the dataset. -->
+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.
 
-This dataset consists of 8,385 molecular dynamics trajectories of small proteins, each containing 1,000 ensemble frames, systematically characterizing the dynamic conformational changes of small proteins 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
 
-Please cite this manuscript for papers that use the DynoDB 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/`: 
+  - `Sheet 1`: Structural and functional annotations for 8,385 entries.
+  - `Sheet 2`: Specific identifiers for the 130 validation systems (ATLAS benchmarks).
   
 ## Dataset Size
 
-
-|  Number of trajectories   | 8,385  |
+|  Dataset Metric   | Value  |
 |  ----  | ----  |
+|  Number of trajectories   | 8,385  |
 | Length per trajectory  | 100 ns |
 | Cumulative simulation time  | 838.5 µs |
 |  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  | ~611GB |
-
+| Storage size  | ~611GB |