wwPDB: Instructions to Journals

<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="description" content="wwPDB: Worldwide Protein Data Bank"> <meta name="author" content="wwPDB.org"> <link rel="shortcut icon" href="/favicon.ico"> <link href="/css/bootstrap-v3.1.1.min.css" rel="stylesheet"> <link href="/tools/font-awesome-4.4.0/css/font-awesome.min.css" rel="stylesheet"> <link href="/css/wwPDB.css?v=4" rel="stylesheet"> <link href='https://fonts.googleapis.com/css?family=Exo+2:600' rel='stylesheet' type='text/css'> <link href='https://fonts.googleapis.com/css?family=Roboto:300, 400,500,700' rel='stylesheet' type='text/css'> <link href='https://fonts.googleapis.com/css?family=Petit+Formal+Script' rel='stylesheet' type='text/css'>  <script async src="https://www.googletagmanager.com/gtag/js?id=G-5ED0CQCXV6"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new 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><a href='/documentation/new-format-for-pdb-ids' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Extended PDB ID With 12 Characters</a></li> <li ><a href='/documentation/file-format' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> File Format</a></li> <li ><a href='/documentation/biocuration' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Deposition & Biocuration Policies</a></li> <li ><a href='/documentation/remediation' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Remediation</a></li> <li class='active'><a href='/documentation/journals' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Instructions to Journals</a></li> </ul> </div> <div class="col-md-9"> <div class="wwpdb-content">  <h1>Instructions to Journals</h1> <p> The wwPDB asks that journals provide the publication date and citation information for structure articles to make the publication of a report and the release of the corresponding PDB structure as simultaneous as possible. Questions not addressed below should be sent to <a href="mailto:deposit- help@mail.wwpdb.org">deposit-help@mail.wwpdb.org.</a> </p> <p> <b>How to Notify the wwPDB that a Structure Should be Released</b> </p> <p> Data in the PDB is released weekly; we are unable to provide data out of cycle. </p> <p> To eliminate any delays between the publication of a report in a journal and the release of the corresponding structure, we request that the paper title, author list, related PDB ID(s), DOI, and publication date be sent to <a href="mailto:deposit-help@mail.wwpdb.org">deposit-help@mail.wwpdb.org</a> two weeks prior to publication. </p> <p> Each week, all files scheduled for release or modification are checked and validated one final time. Authors may be contacted to resolve any issues that may arise while preparing the entries for release. If this is not accomplished in time for release, the entry may be scheduled for a later update. </p> <p> <b>Preferred Instructions to the Author</b> </p> <p> We suggest that journals adopt the policy below for papers describing experimentally- determined, biological macromolecule structures. The deposition of coordinates and experimental data, and their immediate public release at the time of the article's publication, provides the scientific community with the materials needed to fully understand the results presented in the manuscript. </p> <blockquote> <i> <p> For papers describing structures of biological macromolecules, the atomic coordinates and related experimental data (structure factor amplitudes/intensities and/or NMR restraints and chemical shifts) must be deposited at a member site of the <a href="../index.php">Worldwide Protein Data Bank</a>. </p> <p> The PDB ID assigned after deposition should be included in the manuscript. Authors must also submit the <a href="http://www.wwpdb.org/validation/validation-reports" href="_target">wwPDB Full Validation Report</a> (provided after annotation by the wwPDB with Watermark: “<a href="http://www.wwpdb.org/validation/2017/FAQs#types" target="_target">For Manuscript Review</a>”) for review at the time of submission.</p> <p> Authors must agree to release the atomic coordinates and experimental data when the associated article is published. Questions relating to depositions should be sent to <a href="mailto:deposit-help@mail.wwpdb.org">deposit-help@mail.wwpdb.org</a>. </p> <p> Electron microscopy-derived density maps (all averaging methods, including sub-tomogram averaging) must be deposited in EM Data Bank (EMDB; <a href="http://emdb-empiar.org" target="_blank">http://emdb-empiar.org</a>). For electron tomographic studies with no averaging, deposition of one or more representative tomograms in EMDB is strongly recommended. In cases where PDB models have been fitted into EMDB maps, the correspondences between them should be clearly stated. </p> </i> </blockquote> <p> Structures can be cited in the article using the PDB ID: The atomic coordinates and experimental data (code 1abc) have been deposited in the Protein Data Bank (<a href="../index.php">www.wwpdb.org</a>). </p> <p>We encourage the scientific journals to make use of the DOIs issued for each PDB entry by linking to them from the online versions of papers where PDB entries are described or mentioned. For example, the PDB entry 6QW9 can be linked using the following URL: <a href="https://doi.org/10.2210/pdb6qw9/pdb" target=_blank">https://doi.org/10.2210/pdb6qw9/pdb</a>.</p> <p>We suggest that the PDB IDs provided to the journals be validated. Please note that a proper PDB ID is of a format 1ABC (4-characters with the first character being numeral in the range 1- 9, and the last three characters either numerals (in the range 0-9) or letters (in the range A-Z). Alternatively, the PDB ID can be represented in an extended format such as pdb_00001abc, with pdb_ prefix followed by 8 alphanumeric characters (please refer to https://www.wwpdb.org/news/news?year=2021#60fee1500882a5597783cc0a for more details). The internal deposition session ids of a format D_xxxxxxxx (D_ followed by 8 numerals) should not be accepted.</p> <p> <b>wwPDB Data Deposition Policies</b> </p> <p> Biomolecular polymers including polypeptides, polynucleotides, polysaccharides, and their complexes that meet the following criteria are accepted: </p> <ul> <li>For polypeptide structures <ol> <li>all gene products</li> <li>all naturally-occurring peptides that are non-ribosomal in origin</li> <li>all peptidic repeat units of larger polymers (such as fibrous and amyloid polymers)</li> <li>Non-biological synthetic peptides with at least 24 residues within a polymer chain </li> </ol> </li> <li>Polynucleotide structures of four or more residues</li> <li>Polysaccharide structures of four or more residues</li> </ul> <p> Detailed information is available at <a href="policy.php">http://www.wwpdb.org/documentation/policy</a>. </p> <p> <b>wwPDB Data Release Policies</b> </p> <ul> <li>The release status of structures is determined at the time of deposition by the author. Structures on hold are released upon publication of the primary citation. If there is no publication, structures can be released:</li> <ul> <li>upon author request</li> <li>after expiration of the hold period (up to one year).</li> </ul> <li>The status HPUB ("Hold for Publication") is used to indicate that a structure will be released when the corresponding journal article is published.</li> <ul> <li>Publication is considered to be when the article is distributed by the publisher, either in print or electronically.</li> <li>Structures are released when the PDB can confirm that the article corresponds with the entry.</li> </ul> <li>The maximum hold for any structure is one year (even for HPUB structures) from the date of deposition (when a PDB ID is issued).</li>  </ul> <p> <b>How to Check if a Structure Has Been Deposited or Released</b> </p> <p> The status of an entry in the PDB archive may be checked by using the PDB ID in a search at one of these wwPDB sites: <a href="https://www.rcsb.org/" target="_blank">RCSB PDB</a>, <a href="https://www.ebi.ac.uk/pdbe/" target="_blank">PDBe</a>, or <a href="https://pdbj.org/" target="_blank">PDBj</a>. </p> <p> <b>How do I access a validation report for an unreleased entry in order to review a manuscript?</b> </p> <p> Validation reports for newly deposited entries are generated during the annotation process. Reports are made available to depositors, who are responsible for submission to the journal. </p> <p> <b>When is the PDB Archive Updated?</b> </p> <p>The weekly update to the PDB data archive occurs in two phases:</p> <p> Phase I: Every Saturday by 3:00 UTC, for every new entry, wwPDB website provides sequence(s) (amino acid or nucleotide) for each distinct polymer (<a href="/files/new_release_structure_sequence.tsv" target="_blank">new_release_structure_sequence.tsv</a>) and, where appropriate, the InChI string(s) for each distinct ligand (<a href="/files/new_release_structure_nonpolymer.tsv" target="_blank">new_release_structure_nonpolymer.tsv</a>)</p> <p>Phase II: Every Wednesday by 00:00 UTC, all new and modified data entries will be updated at each of the wwPDB FTP sites.</p> <p> <b>What is the deadline for requesting release of entries?</b> </p> <p> PDB entries are processed by the members of the wwPDB (RCSB, PDBe and PDBj). They are either released when the corresponding paper is published (HPUB), released on a particular date (HOLD), or released immediately (REL). </p> <p> Each week, all files scheduled for release or modification are checked and validated one final time. Authors may be contacted to resolve any issues that may arise while preparing the entries for release. </p> <p> When the release of HPUB structures is requested, the PDB staff routinely confirms the primary citation. If this is not accomplished within that release cycle, the entry may be scheduled to be released in a later update. </p> <p> To be included in the next update, any required author correspondence should be sent to the appropriate wwPDB member by noon Thursday (local time): </p> <p> All entries due for release are then transferred to the RCSB PDB for final packaging into the master PDB ftp archive. </p> <p> Requests received after these cutoff times will be processed during the next update cycle. </p> <p> <b>What is the PDB/wwPDB?</b> </p> <p> The Protein Data Bank (PDB) archive is the single repository for macromolecular structural data. </p> <p> The PDB is managed by members of the Worldwide Protein Data Bank (wwPDB) to ensure that the data are freely and publicly available to the global community. </p> <p> The wwPDB sites support systems to deposit data, and public websites and FTP servers to access the data. </p>  </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="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.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 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="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/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbe.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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wwPDB: Instructions to Journals