RosettaCommons/2J-Protein-Couplings

---
license: other
license_name: non-commercial-license-dyna1
license_link: https://github.com/WaymentSteeleLab/Dyna-1/blob/main/LICENSE.txt
tags:
- proteins
- nmr
pretty_name: 2J_Coupling
size_categories:
- n<1K
viewer: true
configs:
- config_name: main
data_files:
- split: 2J_couplings
path: 2J_couplings.csv
---

<h1>2J-Protein-Coupling Dataset</h1>

This data set was curated from the paper below accessed through the Biological Magnetic Resonance Data Bank (BMRB). There are a total of 3999 2J coupling taken from 5 different proteins and up to 10 different experiments. This dataset contains information regarding PDB ID, Sequence, 2J coupling data of 15N, 13C, and 1H. Data was curated and organized into this set of the five papers below, with the addition of the sequence taken from the Protein Data Bank.

<h2>Raw Data Source</h2>
<p>This dataset was curated from the following research paper:</p>
<ul>

<p> Schmidt, Jurgen; Hua, Yixun; Lohr, Frank. "Correlation of (2)J couplings with protein secondary structure." Proteins 78, 1544-1562 (2010).
<p> https://doi.org/10.1002/prot.22672 </p>

</ul>

<h2>Quickstart Usage</h2>

<h3>1. Install the datasets Library</h3>
<p>From the terminal / command line:</p>
<pre><code>pip install datasets
</code></pre>

<p>In Jupyter Notebook, prefix with <code>!</code>:</p>
<pre><code>!pip install datasets
</code></pre>

<h3>2. Load the Dataset in Python</h3>
<pre><code>from datasets import load_dataset

dataset_protein = load_dataset(
"RosettaCommons/2J-Protein-Coupling",
data_files="Protein/*.csv"
)
</code></pre>

<h3>3. Access Dataset Columns</h3>
<pre><code># Example: Get protein sequences and lengths
sequences = dataset_protein["train"]["sequence"]
lengths = dataset_protein["train"]["sequence_length"]

print(sequences[:5])
print(lengths[:5])
</code></pre>

<h2>Dataset Description</h2>
<p>Each row represents a single polymer chain within a larger macromolecular assembly. Key fields include:</p>
<ul>
<li><strong>entry_id</strong>: ID from the Biological Magnetic Resonance Data Bank (BMRB)</li>
<li><strong>file_name</strong>: Named by experiment and entry_id</li>
<li><strong>sequence_length</strong>: Length of the protein sequence</li>
<li><strong>sequence</strong>: Protein sequence in single-letter amino acid code</li>
<li><strong>experiment_code</strong>: Type of experiment</li>
<li><strong>num_measurements</strong>: Number of experiments recorded for each protein</li>
</ul>

### Citation
```
@article{Schmidt2010,
title = {Correlation of 2J couplings with protein secondary structure},
volume = {78},
ISSN = {1097-0134},
url = {http://dx.doi.org/10.1002/prot.22672},
DOI = {10.1002/prot.22672},
number = {6},
journal = {Proteins: Structure, Function, and Bioinformatics},
publisher = {Wiley},
author = {Schmidt, J\"{u}rgen M. and Hua, Yixun and L\"{o}hr, Frank},
year = {2010},
month = feb,
pages = {1544–1562}
}
```

<i>_This dataset was curated by Nicolas Langdon (<a href="mailto:[e-mail]">[e-mail]</a>) from the five original papers listed above._</i>