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<h1 id="eternabench">EternaBench<a class="headerlink" href="#eternabench" title="Permanent link">&para;</a></h1>
<p><img alt="EternaBench" src="https://eternagame.org/sites/default/files/thumb_eternabench_paper.png" /></p>
<p>EternaBench is a database comprising the diverse high-throughput structural data gathered through the crowdsourced RNA design project Eterna, to evaluate the performance of a wide set of structure algorithms.</p>
<h1 id="eternabench-chemmapping">EternaBench-ChemMapping<a class="headerlink" href="#eternabench-chemmapping" title="Permanent link">&para;</a></h1>
<p><img alt="EternaBench-ChemMapping" src="https://eternagame.org/sites/default/files/thumb_eternabench_paper.png" /></p>
<p>EternaBench-ChemMapping is a synthetic RNA dataset comprising 12,711 RNA constructs that have been chemically mapped using SHAPE and MAP-seq methods.
These RNA sequences are probed to obtain experimental data on their nucleotide reactivity, which indicates whether specific regions of the RNA are flexible or structured.
The dataset provides high-resolution, large-scale data that can be used for studying RNA folding and stability.</p>
<h2 id="disclaimer">Disclaimer<a class="headerlink" href="#disclaimer" title="Permanent link">&para;</a></h2>
<p>This is an UNOFFICIAL release of the <a href="https://github.com/eternagame/EternaBench">EternaBench</a> by Hannah K. Wayment-Steele, et al.</p>
<p><strong>The team releasing EternaBench did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.</strong></p>
<p>This is an UNOFFICIAL release of the <a href="https://github.com/eternagame/EternaBench">EternaBench-ChemMapping</a> by Hannah K. Wayment-Steele, et al.</p>
<p><strong>The team releasing EternaBench-ChemMapping did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.</strong></p>
<h2 id="dataset-description">Dataset Description<a class="headerlink" href="#dataset-description" title="Permanent link">&para;</a></h2>
<ul>
<li><strong>Homepage</strong>: <a href="https://multimolecule.danling.org/datasets/eternabench">https://multimolecule.danling.org/datasets/eternabench</a></li>
<li><strong>Homepage</strong>: <a href="https://multimolecule.danling.org/datasets/eternabench_cm">https://multimolecule.danling.org/datasets/eternabench_cm</a></li>
<li><strong>datasets</strong>: <a href="https://huggingface.co/datasets/multimolecule/eternabench-cm">https://huggingface.co/datasets/multimolecule/eternabench-cm</a></li>
<li><strong>Point of Contact</strong>: <a href="https://biochemistry.stanford.edu/people/rhiju-das/">Rhiju Das</a></li>
</ul>
<p>The dataset includes a large set of synthetic RNA sequences with experimental chemical mapping data, which provides a quantitative readout of RNA nucleotide reactivity. These data are ensemble-averaged and serve as a critical benchmark for evaluating secondary structure prediction algorithms in their ability to model RNA folding dynamics.</p>
<h2 id="example-entry">Example Entry<a class="headerlink" href="#example-entry" title="Permanent link">&para;</a></h2>
<p>| ID | design_name | sequence | structure | reactivity | errors | signal_to_noise |
| 769337-1 | d+m plots weaker again | GGAAAAAAAAAAA&hellip; | ................ | [0.642,1.4853,0.1629, &hellip;] | [0.3181,0.4221,0.1823, &hellip;] | 3.227 |</p>
<table>
<thead>
<tr>
<th>index</th>
<th>design</th>
<th>sequence</th>
<th>secondary_structure</th>
<th>reactivity</th>
<th>errors</th>
<th>signal_to_noise</th>
</tr>
</thead>
<tbody>
<tr>
<td>769337-1</td>
<td>d+m plots weaker again</td>
<td>GGAAAAAAAAAAA&hellip;</td>
<td>................</td>
<td>[0.642,1.4853,0.1629, &hellip;]</td>
<td>[0.3181,0.4221,0.1823, &hellip;]</td>
<td>3.227</td>
</tr>
</tbody>
</table>
<h2 id="column-description">Column Description<a class="headerlink" href="#column-description" title="Permanent link">&para;</a></h2>
<p>The EternaBench dataset consists of the following columns, providing crucial insights for understanding RNA stability for vaccine design:</p>
<ul>
<li>
<p><strong>ID</strong>:
A unique identifier for each RNA sequence entry.</p>
<p><strong>id</strong>:
A unique identifier for each RNA sequence entry.</p>
</li>
<li>
<p><strong>design_name</strong>:
The name given to each RNA design by contributors, used for easy reference.</p>
<p><strong>design</strong>:
The name given to each RNA design by contributors, used for easy reference.</p>
</li>
<li>
<p><strong>sequence</strong>:
The nucleotide sequence of the RNA, using standard bases.</p>
The nucleotide sequence of the RNA molecule, represented using the standard RNA bases:</p>
<ul>
<li><strong>A</strong>: Adenine</li>
<li><strong>C</strong>: Cytosine</li>
<li><strong>G</strong>: Guanine</li>
<li><strong>U</strong>: Uracil</li>
</ul>
</li>
<li>
<p><strong>structure</strong>:
The predicted secondary structure of the RNA, represented using dot-bracket notation.
The structure helps determine the likely secondary interactions within each RNA molecule.</p>
<p><strong>secondary_structure</strong>:
The secondary structure of the RNA represented in dot-bracket notation, using up to three types of symbols to indicate base pairing and unpaired regions, as per bpRNA&rsquo;s standard:</p>
<ul>
<li><strong>Dots (<code>.</code>)</strong>: Represent unpaired nucleotides.</li>
<li><strong>Parentheses (<code>(</code> and <code>)</code>)</strong>: Represent base pairs in standard stems (page 1).</li>
<li><strong>Square Brackets (<code>[</code> and <code>]</code>)</strong>: Represent base pairs in pseudoknots (page 2).</li>
<li><strong>Curly Braces (<code>{</code> and <code>}</code>)</strong>: Represent base pairs in additional pseudoknots (page 3).</li>
</ul>
</li>
<li>
<p><strong>reactivity</strong>:
A list of floating-point values that provide an estimate of the likelihood of the RNA backbone being cut at each nucleotide position.
These values help determine the stability of the RNA structure under various experimental conditions.</p>
A list of normalized reactivity values for each nucleotide, representing the likelihood that a nucleotide is unpaired.
High reactivity indicates high flexibility (unpaired regions), and low reactivity corresponds to paired or structured regions.</p>
</li>
<li>
<p><strong>errors</strong>:
Arrays of floating-point numbers indicating the experimental errors corresponding to the measurements in the <strong>reactivity</strong>.
These values help quantify the uncertainty in the degradation rates and reactivity measurements.</p>
Arrays of floating-point numbers indicating the experimental errors corresponding to the measurements in the <strong>reactivity</strong>.
These values help quantify the uncertainty in the degradation rates and reactivity measurements.</p>
</li>
<li>
<p><strong>signal_to_noise</strong>:
The signal-to-noise ratio calculated from the reactivity and error values, providing a measure of data quality.</p>
</li>
</ul>
<h2 id="variations">Variations<a class="headerlink" href="#variations" title="Permanent link">&para;</a></h2>
<p>This dataset is available in two subsets:</p>
<h2 id="related-datasets">Related Datasets<a class="headerlink" href="#related-datasets" title="Permanent link">&para;</a></h2>
<ul>
<li><a href="https://huggingface.co/datasets/multimolecule/eternabench-cm">EternaBench-CM</a></li>
<li><a href="https://huggingface.co/datasets/multimolecule/eternabench-cm">EternaBench-ChemMapping</a></li>
<li><a href="https://huggingface.co/datasets/multimolecule/eternabench-switch">EternaBench-Switch</a></li>
</ul>
<h2 id="license">License<a class="headerlink" href="#license" title="Permanent link">&para;</a></h2>
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