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<!DOCTYPE html>
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<meta itemprop="description" content="RNA-Puzzles a community-wide blind evaluation of RNA 3D structure prediction." />
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<h2>RNA-Puzzles</h2> is a collective experiment for blind RNA structure prediction.<br/>
The sequence of a solved RNA structure is confidentially communicated to participating modelling groups a couple of weeks prior to publication. The results are assessed and presented in common publications involving structuralists and modellers.</br>
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<h3 class="panel-title">Aims of the project</h3>
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<li>To determine the capabilities and limitations of current computational methods of 3D RNA structure prediction based on sequence;</li>
<li>To assess progress made and to improve assessment protocols and methods;</li>
<li>To identify whether there are specific bottlenecks that hold back progress;</li>
<li>To promote the available methods and guide potential users in the choice of suitable tools;</li>
<li>To encourage the RNA structure prediction community in their efforts to improve the current tools and to make automated prediction tools available;</li>
<li>To explore the underlying mechanism of ligand-RNA binding and associated conformational changes.</li>
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<div class="panel-heading"><h3 class="panel-title">Basic Rules <a style="color:red">(PLEASE READ CAREFULLY)</a></h3></div>
<li>Confidential agreement required from new users: "I will use the provided sequence data for prediction purposes only. I will not distribute the sequences in any form outside my working group."</li>
<li>It is strongly recommended to avoid assessment error that all the predictions be formatted in standard <b><a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1992.pdf">PDB format</a></b>. We provide a python script <b><a href="https://chichaumiau.github.io/RNA-Puzzles_format/">here</a></b> for generating standard PDB format files into which the coordinates need to be replaced by the predictors. </li>
<li>Please name the submission file without space in the file name. The suggested names are: PZ#_Method.pdb for web servers and PZ#_GroupName.pdb for human predictors. </li>
<li>RNA chains should be named in alphabetical order: A for the first chain, B for the second chain, and so on. </li>
<li>Up to <b>FIVE</b> prediction models should be submitted as the final results for each puzzle from each prediction method. Each prediction group can submit results from several prediction methods (automatic or manual, etc.). </li>
<li>Please put all prediction models together in one PDB file as in the NMR format (Separate models by lines: "MODEL n" and "ENDMDL"). </li>
<li>For submission, please either use the online <a href="http://www.rnapuzzles.org/open-puzzle/">registration and submission</a> portal (see the open-puzzle tag: http://www.rnapuzzles.org/open-puzzle/) or send us an <b><a href="mailto:e.westhof@ibmc-cnrs.unistra.fr?cc=ibmc.cnrs@gmail.com&subject=RNA-Puzzles%20Submission">email</a></b> (Please send an email to e.westhof@ibmc-cnrs.unistra.fr and cc. ibmc.cnrs@gmail.com).</li>
<li>For structure comparison metrics, please refer to RNA-Puzzles toolkit at <a href="https://chichaumiau.github.io/rnapuzzlestoolkit">https://chichaumiau.github.io/rnapuzzlestoolkit</a>. Please find the reference at <a href="https://pubmed.ncbi.nlm.nih.gov/31799609/">Nucleic Acids Res. 2020 Jan 24;48(2):576-588</a>. To use evaluation metrics in CASP15, please also refer to the repos: <a href="https://github.com/DasLab/casp-rna">https://github.com/DasLab/casp-rna</a> and <a href="https://github.com/DasLab/CASP15_RNA_EM">https://github.com/DasLab/CASP15_RNA_EM</a>. The reference can be found at <a href="">biorxiv</a>.</li>
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<div class="panel-heading"><h3 class="panel-title">Call for participants</h3></div>
<li>We hope more structural biologists can help us in providing more crystallographic, cryo-EM or NMR structures. Any kind of RNA related structure information is encouraged. Anyone who may have a RNA structure ready for publication please contact <a href="mailto:e.westhof@ibmc-cnrs.unistra.fr?cc=ibmc.cnrs@gmail.com&subject=[RNA-Puzzles]%20Structure%20Provide">us</a> (Please send an email to e.westhof@ibmc-cnrs.unistra.fr and cc. ibmc.cnrs@gmail.com).</li>
<li>We encourage more predictors who are interested in RNA structure prediction to take part in this compitition to push forward the field. Anyone who is interested please send us an <a href="mailto:e.westhof@ibmc-cnrs.unistra.fr?subject=[Help]%20RNA-Puzzles&cc=ibmc.cnrs@gmail.com">email</a> (Please send an email to e.westhof@ibmc-cnrs.unistra.fr and cc. ibmc.cnrs@gmail.com).</li>
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<a href="/blog/2026/04/02/PZ74-PZ79-Update-Support-for-Standard-DNA-Residue-Names/" itemprop="url">PZ74–PZ79 Update: Support for Standard DNA Residue Names</a>
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<a href="/blog/2017/11/18/PZ39/" itemprop="url">Puzzle 39</a>
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<a href="/blog/2017/11/18/PZ38/" itemprop="url">Puzzle 38</a>
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<a href="/blog/2017/11/18/PZ37/" itemprop="url">Puzzle 37</a>
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<a class='category' href='/blog/categories/results/'>results</a>
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<a href="/blog/2017/11/18/PZ36/" itemprop="url">Puzzle 36</a>
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<h1>RNA-Puzzles</h1>
<p>A collective blind evaluation of RNA three-dimensional structure prediction</p>
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