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crosslinking mass spectrometry-based structure models</a></td> </tr> <tr> <td class='date'>01/29/2025</td> <td><a href='#678fc87374852a2c7d916ddc'>Take the PDBx/mmCIF User Guide Survey and Win!</a></td> </tr> <tr> <td class='date'>01/16/2025</td> <td><a href='#677880ea44a8c95814022eb9'>PDB-Dev now PDB-IHM</a></td> </tr> <tr> <td class='date'>01/05/2025</td> <td><a href='#675091cd6d0704f88d1d2647'>Time-stamped Copies of PDB and EMDB Archives</a></td> </tr> </table> <div class='news'> <a class='anchor' name='67be07c041f3196e2505ea6d'></a><a class='anchor' name='11-March-2025'></a> <p class='wwpdb-page-news-date'>03/11/2025</p> <h2>Poster Prize Awarded at The Biophysical Society Meeting</h2><p>The wwPDB Foundation made an award for an outstanding student presentation at the <a href='https://www.biophysics.org/2025meeting#/'>2025 Biophysical Society Meeting (February 15-19, Los Angeles, CA)</a>.</p><div class='row'><div class='pull-left' style='margin: 12px;'><a href='https://cdn.rcsb.org/news/2025/hsiang-ling-poster.jpg' data-toggle='lightbox' data-title='' data-footer=''><img src='https://cdn.rcsb.org/news/2025/hsiang-ling-poster.jpg' alt='<I>Hsiang-Ling Huang</I>' class='img-responsive' style=''></a><small><I>Hsiang-Ling Huang</I></small></div></div><p><I>Mechanisms of dysferlin-mediated membrane repair in health and disease</I><BR> Hsiang-Ling Huang (1), Giovanna Grandinetti (1,2), Sarah M. Heissler (1), Krishna Chinthalapudi (1)<BR> (1) Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University College of Medicine, United States<BR> (2) Center for Electron Microscopy and Analysis, The Ohio State University, United States</p><p>Many thanks to The Biophysical Society organizers and poster prize judges for making this award possible.</p><p><a href=https://foundation.wwpdb.org/index.html>The wwPDB Foundation</a> was established in 2010 to raise funds in support of the outreach activities of the wwPDB. The Foundation raised funds to help support PDB50 events, workshops, and educational publications. The Foundation is chartered as a 501(c)(3) entity exclusively for scientific, literary, charitable, and educational purposes.</p><p>The wwPDB Foundation is grateful for our industrial sponsors: <a href=https://foundation.wwpdb.org/donations.html>Discngine</a>. Individual sponsorships are also available.</p><p>Consider supporting the next 50 years of PDB's spirit of openness, cooperation, and education with a <a href=https://foundation.wwpdb.org/donations.html>donation to the wwPDB Foundation</a>.</p> </div> <div class='top-link'><a href='#top'><span class='glyphicon glyphicon-chevron-up'></span> Top</div> <div class='news'> <a class='anchor' name='67c4575365ecc77724b625ed'></a><a class='anchor' name='10-March-2025'></a> <p class='wwpdb-page-news-date'>03/10/2025</p> <h2>New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models</h2><div class='row'><div class='pull-left' style='margin: 12px;'><img src='https://cdn.rcsb.org/news/2025/figure.png' alt='<I>New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models</I>' class='img-responsive' style=''><small><I>New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models</I></small></div></div><p>We are pleased to announce the release of updated validation reports (version 2) for structures determined using integrative and hybrid methods (IHM) archived in the <a href=https://files.wwpdb.org/pub/>PDB-IHM branch</a> of the PDB archive. These reports are available in the archive and on the <a href='https://pdb-ihm.org/'>PDB-IHM website</a>. IHM Validation software v2 is now integrated into the PDB-IHM <a href='https://data.pdb-ihm.org/'>deposition and curation system</a> to support validation of new depositions. For detailed information on IHM Validation and v2 updates, please refer to the <a href='https://pdb-ihm.org/about_validation.html'>help page</a> and <a href='https://pdb-ihm.org/validation_help.html'>user guide</a>. The software is also available for standalone use via <a href='https://github.com/salilab/IHMValidation'>GitHub</a>.</p><p>We thank the <a href=/task/hybrid>wwPDB IHM Task Force</a> members and the broader structural biology community for supporting the development of validation methods for integrative structures.</p><h4>What’s New in Version 2?</h4><p>The latest update extends IHM validation to structures derived from Chemical Crosslinking Mass Spectrometry (Crosslinking-MS) data, in addition to the previously supported Small Angle Scattering (SAS) data. This milestone is the result of close collaboration among the Crosslinking-MS community, <a href='https://www.ebi.ac.uk/pride/'>PRIDE</a> repository, and the PDB-IHM team.</p><p>To support this advancement, we have developed interoperability mechanisms between PDB-IHM and PRIDE, enabling validation of integrative structures based on Crosslinking-MS data. Additionally, <a href='https://www.ebi.ac.uk/pride/archive/crosslinking'>PRIDE Crosslinking</a> now supports submission of complete Crosslinking-MS datasets following the <a href='https://github.com/HUPO-PSI/mzIdentML/blob/master/schema/mzIdentML1.2.0.xsd'>mzIdentML 1.2.0</a> community data standard.</p><p>Furthermore, IHM Validation software v2 uses <a href='https://doi.org/10.1002/pro.3330'>MolProbity</a> version 4.5.2 and the <a href='https://doi.org/10.1093/bioinformatics/btac400'>PrISM</a> software for precision analysis.</p><h4>Next Steps for Depositors</h4><p>We encourage depositors working with Crosslinking-MS-based integrative structures to:</p><ul><li> Submit complete datasets to PRIDE Crosslinking following the provided <a href="https://www.ebi.ac.uk/pride/markdownpage/crosslinking">guidelines</a>.</li><li> Cross-reference PRIDE Crosslinking datasets in PDB-IHM depositions to enable robust validation.</li></ul> </div> <div class='top-link'><a href='#top'><span class='glyphicon glyphicon-chevron-up'></span> Top</div> <div class='news'> <a class='anchor' name='678fc87374852a2c7d916ddc'></a><a class='anchor' name='29-January-2025'></a> <p class='wwpdb-page-news-date'>01/29/2025</p> <h2>Take the PDBx/mmCIF User Guide Survey and Win!</h2><p>Please take this <a href='https://rutgers.ca1.qualtrics.com/jfe/form/SV_ebusbrMCmLbB0WO'>brief survey</a> about the <a href=https://mmcif.wwpdb.org/docs/user-guide/guide.html>PDBx/mmCIF User Guide</a> to help us gain insights into the Guide’s usage and identify areas for future improvement.</p><div class='row'><div class='pull-left' style='margin: 12px;'><a href=https://mmcif.wwpdb.org/docs/user-guide/guide.html><img src='https://cdn.rcsb.org/news/2024/pdbx-graphic0617.png' alt='<I>Benefits of the PDBx/mmCIF ecosystem</I>' class='img-responsive' style=''></a><small><I>Benefits of the PDBx/mmCIF ecosystem</I></small></div></div><p>Your feedback is highly valued.</p><p>Respondents can enter a drawing for a chance to win a prize from the wwPDB.</p><p>The survey will remain open until February 28, 2025.</p> </div> <div class='top-link'><a href='#top'><span class='glyphicon glyphicon-chevron-up'></span> Top</div> <div class='news'> <a class='anchor' name='677880ea44a8c95814022eb9'></a><a class='anchor' name='16-January-2025'></a> <p class='wwpdb-page-news-date'>01/16/2025</p> <h2>PDB-Dev now PDB-IHM</h2><div class='row'><div class='pull-left' style='margin: 12px;'><img src='https://cdn.rcsb.org/news/2024/ihm-full.png' alt='<I>Integrative structures are available at wwPDB.org and the PDB archive</I>' class='img-responsive' style=''><small><I>Integrative structures are available at wwPDB.org and the PDB archive</I></small></div></div><p>Structures of many large macromolecular assemblies are now being determined using integrative approaches, wherein information derived from multiple experimental and computational methods is combined to compute their three-dimensional structures. PDB-IHM (formerly PDB-Dev) is a system for archiving and disseminating structures determined using integrative or hybrid methods (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR).</p><p>In August 2024, PDB-Dev was unified with the PDB to deliver integrative structures alongside experimental structures in the <a href=https://files.wwpdb.org/pub/>PDB archive</a>. With unification, integrative structures are assigned PDB accession codes and Digital Object Identifiers (DOIs), annotated as IHM structures, and can be accessed from the PDB archive, PDB DOI links (e.g., DOI: <a href='https://doi.org/10.2210/pdb8zzc/pdb'>10.2210/pdb8zzc/pdb</a>), and the <a href='https://pdb-ihm.org/'>PDB-IHM website</a>. Now part of the PDB infrastructure, PDB-Dev has been rebranded as <B>PDB-IHM</B>, denoting IHM structures archived in the PDB.</p><p>Integrative structures can be deposited through the <a href='https://data.pdb-ihm.org/'>PDB-IHM deposition portal</a> and accessible from the <a href=https://deposit.wwpdb.org/>wwPDB OneDep home page</a>. They are processed in parallel to the <a href=https://deposit.wwpdb.org/>wwPDB OneDep system</a>. Structures processed by PDB-IHM are released synchronously with PDB structures weekly on Wednesdays at 00:00 UTC.</p><p>In the future, the wwPDB partners, including Research Collaboratory for Structural Bioinformatics Protein Data Bank (<a href='https://rcsb.org/'>RCSB PDB</a>) in the United States, Protein Data Bank in Europe (<a href='https://ebi.ac.uk/pdbe/'>PDBe</a>), and Protein Data Bank Japan (<a href='https://pdbj.org/'>PDBj</a>), will disseminate integrative structures on their respective websites.</p><p>We look forward to supporting the structural biology community with depositing integrative structures to <a href='https://pdb-ihm.org/'>PDB-IHM</a>.</p><p>Questions or feedback? Contact <a href='mailto:deposit-help@mail.wwpdb.org'>deposit-help@mail.wwpdb.org</a> or <a href='mailto:heldesk@pdb-ihm.org'>heldesk@pdb-ihm.org</a>.</p> </div> <div class='top-link'><a href='#top'><span class='glyphicon glyphicon-chevron-up'></span> Top</div> <div class='news'> <a class='anchor' name='675091cd6d0704f88d1d2647'></a><a class='anchor' name='05-January-2025'></a> <p class='wwpdb-page-news-date'>01/05/2025</p> <h2>Time-stamped Copies of PDB and EMDB Archives</h2><div class='row'><div class='pull-left' style='margin: 12px;'><img src='https://cdn.rcsb.org/news/2022/camera-iocn.png' alt='<I>New archive snapshots are available. </I>' class='img-responsive' style=''><small><I>New archive snapshots are available. </I></small></div></div><p>A snapshot of the PDB Core archive (<a href=https://files.wwpdb.org/>https://files.wwpdb.org/, <a href='https://s3.rcsb.org'>https://s3.rcsb.org</a>) as of January 1, 2025 has been added to <a href="https://s3snapshots.rcsb.org/">https://s3snapshots.rcsb.org/</a>, snapshots.rcsb.org (rsync -rlpy -a -v --delete snapshots.rcsb.org:: .), and <a href="ftp://snapshots.pdbj.org">ftp://snapshots.pdbj.org</a>. Snapshots have been archived annually since 2005 to provide readily identifiable data sets for research on the PDB archive.</p><p>The directory 20250101 includes the 229,564 experimentally-determined structure and experimental data available at that time. Atomic coordinate and related metadata are available in PDBx/mmCIF, PDB, and XML file formats. The date and time stamp of each file indicates the last time the file was modified. The snapshot of PDB Core Archive is 1,437 GB.</p><p>A snapshot of the EMDB Core archive (<a href="ftp://ftp.ebi.ac.uk/pub/databases/emdb/">ftp://ftp.ebi.ac.uk/pub/databases/emdb/</a>) as of January 01, 2025 can be found in <a href="ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20250101/">ftp://ftp.ebi.ac.uk/pub/databases/emdb_vault/20250101/</a> and <a href="ftp://snapshots.pdbj.org/20250101/">ftp://snapshots.pdbj.org/20250101/</a>. The snapshot of EMDB Core Archive contains map files and their metadata within XML files for both released and obsoleted entries (41,367 and 301, respectively) and is 21 TB in size.</p> </div> <div class='top-link'><a href='#top'><span class='glyphicon glyphicon-chevron-up'></span> Top</div>  </div> </div> </div> <br> <footer class="footer"> <div class="container-fluid hidden-print" style="position: relative;"> <div class="row topFooter tinyPad"> <div class="ScreenLimitFooter"> <div class="col-sm-4"> <div class="smallMarginTop"> <a href="https://www.facebook.com/pages/Worldwide-PDB/223648640998643" target="_blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/facebook.png" width="24" height="24"></a> <a href="https://www.youtube.com/channel/UCgM7zpapumhWHDMV11FIz0Q" target="_blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/youtube-logo.png" width="24" height="24"></a> <a href="#"><img alt="RSS Feed for the Latest News" src="https://cdn.rcsb.org/wwpdb/img/core/rss.png" width="24" height="24"></a> <a href="mailto: info@wwpdb.org"><img src="https://cdn.rcsb.org/wwpdb/img/core/mail.png" width="24" height="24"></a> </div> <div class="smallMarginTop"> <a href="/news/news.php"> <p><a href="/news/news.php">News & Announcements</a></p> </a> </div> <div> <p><a href="https://lists.wwpdb.org/list/pdb-l.lists.wwpdb.org">Community Bulletin Board</a></p> </div> <div><a class='brand hidden-desktop' href='http://foundation.wwpdb.org/' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/core/wwpdb-foundation-logo.png" class="logoLimit smallMarginTop"></a></div> </div> <div class="col-sm-4"> <div class="tinyMarginTop"> <h4><a class="h4-link" href="/download/downloads.php">Download Archive</a></h4> </div> <div class="smallMarginTop"> <a href="https://files.wwpdb.org/pub/pdb/">RCSB PDB</a> | <a href="https://ftp.ebi.ac.uk/pub/databases/pdb/">PDBe</a> | <a href="https://ftp.pdbj.org/pub/pdb/">PDBj</a> <br> <a href="/download/downloads.php">Instructions</a> </div> <div class="row"> <div class="col-sm-4"> <div class="tinyMarginTop"> <h4>Archive Snapshots</h4> </div> <div class="smallMarginTop"> <a href="https://s3snapshots.rcsb.org">RCSB PDB (https)</a> | <a href="ftp://snapshots.pdbj.org/">PDBj</a> </div> </div>  </div> </div> <div class="col-sm-3"> <h4> Cite wwPDB: </h4> <div class="smallMarginTop"> <em>Nature Structural Biology</em> <strong>10</strong>, 980 (2003)<br> <a href="http://dx.doi.org/10.1038/nsb1203-980" target="_blank">doi: 10.1038/nsb1203-980</a> <p class="tinyMarginTop"><a href="/about/publications.php">More publications</a></p> </div> </div> <div class="row" style="padding: 40px 0px 10px 10px"> <div class="col-sm-7"> <div class="tinyPad"> <h4>wwPDB Members:</h4> </div> <div class="col-sm-2 tinyPad"><a href="https://www.ebi.ac.uk/pdbe/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbe.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.rcsb.org/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/rcsb-pdb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="http://bmrb.io/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/bmrb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.pdbj.org/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbj.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.ebi.ac.uk/pdbe/emdb/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/emdb.png" class="logoLimit img-responsive"></a></div> </div> <div class="col-sm-1"><br></br></div> <div class="col-sm-4"> <div class="row"> <div class="col-xs-6"> <a href='http://www.CoreTrustSeal.org' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/homepage/CoreTrustSeal-logo-transparent-small.png" class='img-responsive seal' style="border-right: 1px solid #666; 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