PDB-IHM

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margin-right: 10px;" ><img src="/images/search.svg" alt="search" /></button> </form>   <p class="my-2"><a href="#" style="color:#FFF;" data-toggle="modal" data-target="#exampleModalCenter"><small>Search Tips</small></a></p>  <div class="modal fade" id="exampleModalCenter" tabindex="-1" role="dialog" aria-labelledby="exampleModalCenterTitle" aria-hidden="true"> <div class="modal-dialog modal-dialog-centered" role="document"> <div class="modal-content"> <div class="modal-header"> <h5 class="modal-title" id="exampleModalLongTitle">Search Tips</h5> <button type="button" class="close" data-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body"> <h6 style="color: #669966;"><b>Keyword Search</b></h6> <p>Search can be carried out using keywords such as</p> <ul> <li>macromolecular names (e.g., Exosome, p53)</li> <li>accession codes (e.g., PDBDEV_00000012, PDBDEV_00000014)</li> <li>experimental methods used (e.g., NMR, 3DEM, Crosslinking-MS)</li> <li>author names (e.g., Sali, Bonvin)</li> <li>software used (e.g., IMP, HADDOCK, ROSETTA)</li> </ul> <hr/> <h6 style="color: #669966;"><b>Boolean Search</b></h6> <p>Boolean operators are supported. </p> <ul> <li> AND (e.g., Kim AND Crosslinking-MS) </li> <li> OR (e.g., IMP OR HADDOCK) </li> <li> NOT (e.g., ROSETTA NOT Crosslinking-MS) </li> </ul> <hr/> <h6 style="color: #669966;"><b>Wild Card</b></h6> <p>Wild card symbol can be used to handle truncations. </p> <ul> <li> nup* can be used to search for all keywords that start with the phrase 'nup' (e.g., nup82, nup84, nup133). </li> <li> *trans* can be used to search for all keywords that contain the phrase 'trans' (e.g., methyltransferase, transcription). </li> <li> *some can be used to search for all keywords that end with the phrase 'some' (e.g., BBSome, exosome, nucleosome, proteasome). </li> </ul> <hr/> <h6 style="color: #669966;"><b>Phrase Search</b></h6> <p>Search for exact phrases can be carried out using single quotes (e.g., 'Nucleotide excision repair complex'). </p> <hr/> <h6 style="color: #669966;"><b>Attribute Search</b></h6> <p>Search for specific attributes defined in PDBx/mmCIF and IHM dictionaries can be carried out as follows. </p> <ul> <li>entry.id:*28</li> <li>entry.id:PDBDEV_00000012</li> <li>ihm_cross_link_list.linker_type:CYS</li> </ul> </div> <div class="modal-footer"> <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button> </div> </div> </div> </div>  </div> </nav> <div class="card-body">  <div class="row"> <div class="col-lg-12">  <div class="card-header" style="background-color: #FFF; border:none;"> <h2>All News</h2> <br/>  <div class="accordion" id="accordionExample"> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseTwenty" aria-expanded="false" aria-controls="collapseTwenty"> <b>PDB-Dev rebranded as PDB-IHM</b> </button> </h2> </div> <div id="collapseTwenty" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> November 26, 2024</p> <p align="justify"> In August 2024, PDB-Dev was unified with the PDB to deliver integrative structures alongside archived experimental structures in the PDB archive. Following the unification, PDB-Dev has now been rebranded as PDB-IHM, denoting integrative and hybrid methods (IHM) structures archived in the PDB. With unification, integrative structures are assigned PDB accession codes, annotated as IHM structures, and can be downloaded from the <a href='https://files.wwpdb.org/pub/pdb_ihm/'>PDB archive</a>. 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 web portals. We look forward to the sustained growth of PDB-IHM with more depositions of integrative structures and we will continue to support the emerging needs of the structural biology community. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseNineteen" aria-expanded="false" aria-controls="collapseNineteen"> <b>wwPDB DOIs and DOI Landing Pages for Integrative Structures</b> </button> </h2> </div> <div id="collapseNineteen" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> October 4, 2024</p> <p align="justify"> Integrative structures in PDB-IHM are now available at wwPDB Digital Object Identifier (DOI) landing pages, along with >225,000 experimental structures in the PDB archive. DOI landing pages are available for both released and on-hold entries in PDB-IHM. These pages present basic information about the corresponding integrative structure, offer download of model coordinates and validation files from the PDB archive (<a href=https://files.wwpdb.org/pub/pdb_ihm/>https://files.wwpdb.org/pub/pdb_ihm/</a>), and provide a link to the <a href=https://pdb-ihm.org/>PDB-IHM</a> resource. The PDB-IHM website has been updated to include the newly available links to PDB DOIs on entry pages. </p> <p align="justify"> For an example, visit the DOI landing page for a recently-released integrative structure in the PDB archive via PDB DOI: <a href=https://doi.org/10.2210/pdb9a8n/pdb>https://doi.org/10.2210/pdb9a8n/pdb</a>.</p> <p align="justify"> PDB DOIs issued for each entry are linked from the online versions of papers where PDB IDs are mentioned. Integrative structures are identified on the wwPDB DOI landing pages using the term "Structure Determination Methodology".</p> <p align="justify"> Questions or feedback? Contact <a href='mailto:helpdesk@pdb-ihm.org'>helpdesk@pdb-ihm.org</a>. For more information visit <a href='https://www.wwpdb.org'>wwpdb.org</a>.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseEighteen" aria-expanded="false" aria-controls="collapseEighteen"> <b>PDB Archive Serves Structures Determined by Integrative and Hybrid Methods</b> </button> </h2> </div> <div id="collapseEighteen" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> August 14, 2024</p> <p align="justify"> Structures determined by integrative and hybrid structure determination methods (IHM) are now available alongside experimental structures in the PDB archive. These structures are deposited to and processed by the PDB-IHM system. Users can access and download IHM structures and associated data from the <a href='https://files.wwpdb.org/pub/pdb_ihm/'>PDB archive</a>.</p> <p align="justify"> Currently, holding files in JSON format, validation reports (summary and full reports) in PDF format, and model files in PDBx/mmCIF format are provided.</p> <ul> <li> /pdb_ihm/holdings/ (current holdings, released structures last modified dates, unreleased entries) </li> <li> /pdb_ihm/data/entries/hash/{PDB_id}/validation_reports/ (summary and full validation reports) </li> <li> /pdb_ihm/data/entries/hash/{PDB_id}/structures/ (latest version of model files) </li> <ul> <li> For example, <a href="https://files.wwpdb.org/pub/pdb_ihm/data/entries/zz/8zz1/structures/8zz1.cif.gz">https://files.wwpdb.org/pub/pdb_ihm/data/entries/zz/8zz1/structures/8zz1.cif.gz</a> </li> </ul> </ul> <p align="justify"> Data may be expanded in the future based on community needs. In the near future, IHM data will also be available via wwPDB DOI landing pages and wwPDB partner websites. </p> <p align="justify"> Questions or feedback? Contact <a href="mailto:deposit-help@mail.wwpdb.org">deposit-help@mail.wwpdb.org</a> or <a href="mailto:helpdesk@pdb-ihm.org">helpdesk@pdb-ihm.org</a>. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseSeventeen" aria-expanded="false" aria-controls="collapseSeventeen"> <b>PDB Accession Codes for Integrative Structures</b> </button> </h2> </div> <div id="collapseSeventeen" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> August 14, 2024</p> <p align="justify"> Integrative structures deposited to PDB-IHM will now be issued 4-character PDB accession codes (e.g., 8ZZ1). Going forward all new depositions will only be issued PDB accession codes and PDB-IHM accession codes (e.g., PDBDEV_00000001) will not be issued. </p> <p align="justify"> Existing entries have been remediated to include new PDB accession codes and re-released. Both accession codes, PDB and PDB-IHM (if available), are reported in the <i>database_2</i> category in IHMCIF files. Additionally, <b>integrative</b> method provenance is captured at <i>_struct.pdbx_structure_determination_methodology</i>. Validation reports have been updated based on the PDB accession codes. </p> <p align="justify"> The PDB-IHM website will support search and access of integrative structures using both PDB and PDB-IHM accession codes. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseSixteen" aria-expanded="false" aria-controls="collapseSixteen"> <b>IHMCIF Publication</b> </button> </h2> </div> <div id="collapseSixteen" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> August 14, 2024</p> <p align="justify">IHMCIF, the data standard underpinning the PDB-IHM system, has been published in the 2024 Special Issue on Computation Resources in the Journal of Molecular Biology: Vallat B et al., IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods, J Mol Biol. 2024; 168546. doi: <a href="https://doi.org/10.1016/j.jmb.2024.168546">10.1016/j.jmb.2024.168546</a>. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseFifteen" aria-expanded="false" aria-controls="collapseFifteen"> <b>Updated Validation Reports</b> </button> </h2> </div> <div id="collapseFifteen" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> April 17, 2024</p> <p align="justify"> We are excited to share that we have updated PDB-IHM validation reports to version 1.1. The key feature of this update is the integration of the validation report generation workflow with the deposition and curation pipeline. Validation reports are now generated during the submission process, along with the issue of accession codes, making these reports available for depositors to review and share pre-release. Other changes include: </p> <ul> <li> Update of MolProbity to version 4.5.2 </li> <li> Minor changes to the presentation of SAS plots </li> <li> Better support for sasCIF format </li> </ul> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseFourteen" aria-expanded="false" aria-controls="collapseFourteen"> <b>CASP16 Call for Targets</b> </button> </h2> </div> <div id="collapseFourteen" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> April 17, 2024</p> <p align="justify"> <a href='https://predictioncenter.org/index.cgi'>CASP</a> (Critical Assessment of protein Structure Prediction) challenges are held every two years. The CASP organizers are now requesting targets for the upcoming <a href='https://predictioncenter.org/casp16/index.cgi'>2024 CASP16</a> challenge in the following categories. </p> <ul> <li> Single protein structures </li> <li> Protein complexes </li> <li> Nucleic acids structures and complexes </li> <li> Organic ligand-protein complexes </li> <li> Ensembles of macromolecule conformations </li> <li> Integrative modeling </li> </ul> <p> CASP is only possible with the generous participation of the experimental structural biology community in providing suitable targets. CASP targets can be directly submitted to CASP organizers or to the PDB. For more information regarding these submissions, please visit the <a href='https://predictioncenter.org/casp16/index.cgi'>CASP16 website</a> or the <a href='https://www.wwpdb.org/news/news?year=2024#6610191172841524659883f5'>wwPDB news site</a>. </p> <p> We welcome submission of CASP targets belonging to the <b> integrative modeling </b> category to PDB-IHM. Please notify the submission of CASP targets to the PDB-IHM team via email at <a href="mailto:helpdesk@pdb-ihm.org">helpdesk@pdb-ihm.org</a>. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseThirteen" aria-expanded="false" aria-controls="collapseThirteen"> <b>New Deposition API</b> </button> </h2> </div> <div id="collapseThirteen" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> January 29, 2024</p> <p align="justify">Starting January 22nd 2024, PDB-IHM accepts automated depositions of integrative structures via an API. Depositors can use a command line interface (CLI) tool to upload IHMCIF files and create new entries for submission. The tool has been implemented using the <a href='https://docs.derivacloud.org/deriva-py/index.html'>deriva-py</a> python API provided by the <a href='https://docs.derivacloud.org/platform.html'>DERIVA</a> scientific asset management platform. The CLI tool is particularly useful for bulk uploads and for creating multiple entries belonging to a collection. Please refer to our deposition <a href='https://docs.google.com/document/d/1577tJoeXxY5MtolMHzJ5000b-dz2M8JrONAyhZRvXVc/edit#heading=h.afb9s1ktd055'>documentation</a> for more information.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseTwelve" aria-expanded="false" aria-controls="collapseTwelve"> <b>New feature - structure collections!</b> </button> </h2> </div> <div id="collapseTwelve" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> March 28, 2023</p> <p align="justify">The PDB-IHM team is excited to announce a new feature - structure collections - to better reflect the links between structures generated within the scope of a single research project, investigation, or publication. With increasing numbers of structures generated through high-throughput experimental methods and artificial intelligence-based computational tools, such as <a href='https://doi.org/10.1038/s41586-021-03819-2'>AlphaFold</a> and <a href='https://doi.org/10.1126/science.abj8754'>RoseTTAFold</a>, structure collections allow for a convenient way of linking related entries. A set of entries can be identified as belonging to a collection during the deposition process. A collection identifier is issued during biocuration, and a list of associated entries can be obtained at any time by querying the collection identifier.</p> <p align="justify">We thank Andrea Graziadei from the <a href='https://www.rappsilberlab.org/'>Rappsilber lab</a> for helping us implement and test structure collections. Users are encouraged to explore the first collection of <a href='https://pdb-ihm.org/solrsearch.html?query=PDBDEV_G_1000001'>entries</a> in PDB-IHM to learn more about this feature. The accompanying <a href='https://doi.org/10.1038/s41587-023-01704-z'>paper</a> describes the development of a novel integrative modeling method using in-cell photo crosslinking mass spectrometry and deep learning.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseEleven" aria-expanded="false" aria-controls="collapseELeven"> <b>First 100 structures in the PDB-IHM!</b> </button> </h2> </div> <div id="collapseEleven" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> October 1, 2022</p> <p align="justify">We are proud to announce an important milestone for PDB-IHM - the first 100 entries are released to the public. This achievement is a result of the continued collaboration among the <a href='https://pdb-ihm.org/about.html'>PDB-IHM team</a>, members of the <a href='http://www.wwpdb.org/task/hybrid'>wwPDB IHM task force</a>, wwPDB leadership, <a href='https://www.rcsb.org/pages/team'>RCSB PDB team members</a>, and our pioneer depositors, who were the first to realize the importance of sharing the results of integrative structural biology investigations. The PDB-IHM project is funded by the United States <a href='https://www.nsf.gov'>National Science Foundation</a>.</p> <p align="justify">The first 100 entries also offer us a glimpse of the complex landscape of modern integrative modeling. While experimental models used with chemical cross-linking are a leading category, techniques such as three-dimensional electron microscopy (3DEM), small angle solution scattering (SAS), Forster resonance enery transfer (FRET), and others, together with powerful AI-based methods for the de novo structure prediction, give us more than 50(!) unique combinations of datasets used for integrative modeling (see figure below). Because integrative structures provide a unique opportunity to gain insights into how biomolecules function in conditions close to the native, many of these investigations are featured in journals such as Cell, Nature, Science, Proceedings of the National Academy of Sciences, and the Journal of Molecular Biology. </p> <p align="justify">We designed PDB-IHM according to the <a href='https://doi.org/10.1038/sdata.2016.18'>FAIR guiding principles</a> to make the integrative structures of biomolecules Findable, Accessible, Interoperable, and Reusable, and with the your help, we will continue to improve it and provide better archiving and structure validation services to our users.</p> <div class="col-lg-6"> <img src="images/PDB-IHM_Stats_Sep-28-2022.png" style='height: 580px' class="img-thumbnail"> <p><b>Combinations of datasets used for integrative modeling studies and their frequencies in PDB-IHM entries</b></p> </div> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseTen" aria-expanded="false" aria-controls="collapseTen"> <b>First AlphaFold-based structure in PDB-IHM</b> </button> </h2> </div> <div id="collapseTen" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> September 3, 2022</p> <p align="justify">For a long time, the primary sources of starting structures for integrative modeling were experimental structures from the <a href='https://www.wwpdb.org'>Protein Data Bank</a> or computational models generated using various comparative modeling approaches. The recent machine learning revolution has led to the development of modeling methods like <a href='https://doi.org/10.1038/s41586-021-03819-2'>AlphaFold2</a> and <a href='https://doi.org/10.1126/science.abj8754'>RoseTTAFold</a>, and also brought a whole new universe of high-quality predicted structures of proteins. More than 200 million predicted structures of individual proteins and complexes are now available to researchers across multiple databases. Now these structures are finally making their way into integrative modeling. </p> <p align="justify">In <a href='https://pdb-ihm.org/entry.html?PDBDEV_00000141'>PDBDEV_00000141</a>, <a href='https://doi.org/10.1073/pnas.2208144119'>Noone et. al.,</a> report a structure of pentraxin protein PTX3, a member of a family of soluble pattern recognition molecules that form an important part of innate immunity, where they facilitate the response to infections and damage by triggering processes such as inflammation. The complete structure of PTX3 was built by integrative modeling using three-dimensional electron microscopy map, mass spectrometry data, and AlphaFold-based starting models. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseNine" aria-expanded="false" aria-controls="collapseNine"> <b>Validation Reports for Integrative Structures</b> </button> </h2> </div> <div id="collapseNine" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> July 8, 2022</p> <p align="justify">Based on the recommendations of the <a href='https://www.wwpdb.org'>wwPDB </a> <a href='https://www.wwpdb.org/task/hybrid'>IHM TaskForce </a> <a href='https://pubmed.ncbi.nlm.nih.gov/31780431/'>(Berman et al. 2019)</a>, we have developed <a href="/about_validation.html">validation reports</a> for structures archived in PDB-IHM. The first version of the validation reports have been released on July 8th, 2022. Additional <a href='/validation_help.html'>documentation</a> and <a href='/about_validation.html'>information</a> about the validation reports are also provided. </p> <p align="justify">The validation report consists of four categories: (i) model composition, (ii) data quality assessments, (iii) model quality assessments, and (iv) fit to data used to build the model. At present, data quality assessments and fit to data used to build the models are evaluated for models built using Small Angle Scattering (SAS) data based on the <a href='https://pubmed.ncbi.nlm.nih.gov/28876235/'>guidelines</a> published by the <a href='https://www.wwpdb.org/task/sas'>wwPDB SAS validation task force</a>. </p> <p align="justify">Validation of integrative structures is a work in progress and additional criteria for validating models based on different experimental methods (such as FRET, chemical crosslinking, 3DEM) will be incorporated in subsequent versions of the validation report. </p> <p align="justify">Please reach out us via <a href="mailto:helpdesk@pdb-ihm.org">email</a> if you have any questions or comments. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseEight" aria-expanded="false" aria-controls="collapseEight"> <b>Updated Embargo Policy</b> </button> </h2> </div> <div id="collapseEight" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> July 8, 2022</p> <p align="justify">We have updated the embargo (HOLD) policy for structures deposited to PDB-IHM. Following <a href='https://www.wwpdb.org/documentation/policy'>wwPDB policies</a>, entries can be placed on hold for a maximum period of one year from the date of deposition. If an entry remains unreleased at the end of the hold period, it must either be released or withdrawn. All unreleased entries that have been on HOLD for more than a year have been released by June 24th, 2022. The updated embargo policy is effective from July 1st 2022. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseSeven" aria-expanded="false" aria-controls="collapseSeven"> <b>New Deposition and Data Harvesting System</b> </button> </h2> </div> <div id="collapseSeven" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> June 18, 2021</p> <p align="justify">We have developed a new <a href="https://data.pdb-ihm.org">Deposition and Data Harvesting System</a> that provides a web interface for depositors to assemble all the information required for archiving integrative structures in PDB-IHM, generate a compliant mmCIF file, and deposit the structure to PDB-IHM. This includes the submission of integrative structures, associated spatial restraints and starting models used, modeling protocols and metadata information (citations, authors, software, data in external repositories, reference sequence information etc.). </p> <p align="justify">The system provides an automated mechanism for collecting diverse and heterogeneous types of integrative structures and restraint data. It has been developed using the <a href="http://isrd.isi.edu/deriva/">DERIVA</a> scientific asset management platform and is based on the definitions in the <a href="https://github.com/ihmwg/IHMCIF">IHMCIF dictionary</a> and the parent <a href="https://mmcif.wwpdb.org">PDBx/mmCIF</a> dictionary. </p> <p align="justify">A <a href="https://docs.google.com/document/d/1577tJoeXxY5MtolMHzJ5000b-dz2M8JrONAyhZRvXVc/">User Guide</a> has been created with documentation regarding creating accounts and submitting structures. </p> <p align="justify">Users are encouraged to provide any feedback via email to <a href="mailto:helpdesk@pdb-ihm.org">helpdesk@pdb-ihm.org</a>.</p> <p align="justify">The old deposition system that had rudimentary file upload functionality, has been deprecated as of June 3rd, 2022. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseSix" aria-expanded="false" aria-controls="collapseSix"> <b>PDB-IHM Publication</b> </button> </h2> </div> <div id="collapseSix" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> December 15, 2021</p> <p align="justify">Recent updates to PDB-IHM, including the development of a new data harvesting system, have been published in Acta Crystallographica Section D: Vallat B et al., New sytem for archiving integrative structures, Acta Cryst. 2021; D77: 1486-1496. doi:<a href="https://doi.org/10.1107/S2059798321010871">10.1107/S2059798321010871</a></p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFive"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseFive" aria-expanded="false" aria-controls="collapseFive"> <b>BioExcel Webinar</b> </button> </h2> </div> <div id="collapseFive" class="collapse" aria-labelledby="headingFive" data-parent="#accordionExample"> <div class="card-body"> <p> July 2, 2020</p> <p align="justify">Recently, the PDB-IHM team participated in the <a href="https://bioexcel.eu/category/webinar/">BioExcel webinar series</a>. The webinar presentation was titled <b>"PDB-Dev: A prototype system for archiving integrative structures"</b>. The recorded version of the webinar is available on <a href="https://www.youtube.com/watch?v=D_ZllHnTL2w&t=565s">youtube</a>. </p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingFour"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseFour" aria-expanded="false" aria-controls="collapseFour"> <b>Visualization of Structures using Molstar</b> </button> </h2> </div> <div id="collapseFour" class="collapse" aria-labelledby="headingFour" data-parent="#accordionExample"> <div class="card-body"> <p> May 20, 2020</p> <p align="justify">3D visualization of structures using <a href="https://molstar.org/">Molstar</a> is now available on PDB-IHM. Structures in PDB-IHM can be directly visualized from the respective entry pages. Molstar can visualize atomic as well as multi-scale structures. </p> <p align="justify">Integrative structures can also be visualized online using the <a href="https://molstar.org/viewer/">Molstar viewer</a>.</p> <p align="justify"><a href="https://molstar.org/">Molstar</a> is an open collaboration started by <a href="https://www.ebi.ac.uk/pdbe/node/1"> PDBe</a> and <a href="https://www.rcsb.org">RCSB PDB</a> to provide a technology stack for data delivery and analysis tools of macromolecules.</p> <p align="justify"><a href="https://molstar.org/">Molstar</a> is under active development. Please report any issues on the <a href="https://github.com/molstar/molstar">Molstar GitHub site</a>.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingThree"> <h2 class="mb-0"> <button class="btn btn-link" type="button" data-toggle="collapse" data-target="#collapseThree" aria-expanded="true" aria-controls="collapseThree"> <b>Welcome to the Updated PDB-IHM Website</b> </button> </h2> </div> <div id="collapseThree" class="collapse" aria-labelledby="headingThree" data-parent="#accordionExample"> <div class="card-body"> <p> March 4, 2020</p> <p align="justify" >The PDB-IHM web interface has been revamped to provide dynamic, responsive and mobile-friendly web pages. The newly designed website has been made possible due to an overhaul of our backend infrastructure. </p> <p align="justify">The PDB-IHM website now includes a new service that facilitates search and retrieval of integrative structures archived in PDB-IHM. Simple search using macromolecular names (e.g., nuclear pore complex), entry identifiers (e.g., PDBDEV_00000012), experimental methods used (e.g., NMR, 3DEM, Crosslinking-MS), author names (e.g., Sali), software used (e.g., IMP, HADDOCK, ROSETTA), and several other keywords are now supported. Search results can be downloaded as CSV or EXCEL files. </p> <p align="justify">We have also added individual entry pages that provide a summary of the structure (title, description, authors) along with other details regarding the citation, software, input data, and links to related resources and downloading the structure. </p> <p align="justify">We welcome feedback from our users. Please send any comments or suggestions to <a href="mailto:helpdesk@pdb-ihm.org">helpdesk@pdb-ihm.org</a>.</p> </div> </div> </div> <div class="card"> <div class="card-header" id="headingTwo"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseTwo" aria-expanded="false" aria-controls="collapseTwo"> <b>Whitepaper from the Integrative Modeling Community</b> </button> </h2> </div> <div id="collapseTwo" class="collapse" aria-labelledby="headingTwo" data-parent="#accordionExample"> <div class="card-body"> <p> March 4, 2020</p> <p align="justify">In March 2019, a satellite workshop titled “Working towards federating structural models and data” was held at the Biophysical Society Annual meeting in Baltimore, Maryland to assess current progress and discuss further requirements for archiving integrative structures. The primary goal of the workshop was to bring together experts from different scientific communities contributing to integrative structural biology and build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validation of integrative structures. A whitepaper summarizing the outcomes of the workshop was recently published in the journal Structure.</p> <p align="justify">Berman HM et al., Structure. 2019 Dec; 27(12):1745-1759. doi: <a href="https://www.sciencedirect.com/science/article/pii/S0969212619303867?via%3Dihub">10.1016/j.str.2019.11.002.</a></p></div> </div> </div> <div class="card"> <div class="card-header" id="headingOne"> <h2 class="mb-0"> <button class="btn btn-link collapsed" type="button" data-toggle="collapse" data-target="#collapseOne" aria-expanded="false" aria-controls="collapseOne"> <b>Visualization of Structures using <span syle="color: #669966;">ChimeraX</span></b> </button> </h2> </div> <div id="collapseOne" class="collapse" aria-labelledby="headingOne" data-parent="#accordionExample"> <div class="card-body"> <p> March 4, 2020</p> <p align="justify">The multi-scale integrative structures downloaded from PDB-IHM can be visualized using the <a href="https://www.rbvi.ucsf.edu/chimerax/">ChimeraX</a> software.</p> <p align="justify">ChimeraX is under active development. It is recommended to use the <a href="https://www.rbvi.ucsf.edu/chimerax/download.html#daily">Daily Build</a> of ChimeraX for visualization.<p/> <p align="justify">Please refer to the <a href="https://www.rbvi.ucsf.edu/chimerax/download.html#daily">Daily Build Notes</a> for information regarding operating systems currently supported by <a href="https://www.rbvi.ucsf.edu/chimerax/">ChimeraX</a>.</p> <p align="justify">The integrative structures can be downloaded as text files (use right click + save as) and opened on ChimeraX using the "format ihm" command line option along with the complete path to the downloaded file:</p> <p><b> open path/to/myfile.cif format ihm</b></p> <p align="justify">Alternately, the following command can be used to directly visualize an entry from PDB-IHM, eg: PDBDEV_00000010.</p> <p><b>open 10 from pdbdev ignoreCache true</b></p> <br/> <h5>Recent Updates</h5> <p align="justify">The PDB-IHM entry files have been recently updated to comply with updates in the <a href="https://github.com/ihmwg/IHMCIF">IHMCIF dictionary</a>.</p> <p align="justify">Older files downloaded from PDB-IHM will not be supported on the latest ChimeraX. Similarly, the new PDB-IHM files will not be supported on older versions of ChimeraX.</p> <p align="justify">Please download a fresh copy of the file from PDB-IHM and/or clear the ChimeraX cached IHM files (delete ~/Downloads/ChimeraX/PDBDev) for visualizing the updated files with the latest ChimeraX.</p> </div> </div> </div> </div> </div> </div> </div>  </div>  <footer class="page-footer"> <div class="container-fluid"> <div class="row" style="/color:#FFF; background-color: rgba(102,153,102, 0.5); ; padding-top: 10px; padding-bottom: 2px;"> <div class="col-sm-6" style="padding-top: 10px; padding-bottom: 10px;"> <a href="http://www.wwpdb.org/" target="_blank"> <img src="/images/wwpdb-logo11.png" alt="wwpdb" height="35px" width="160px"/></a> </div>  <div class="col-sm-6"> <div class="float-right text-right"> <p style="margin-bottom: 0px; margin-right: 0px;color: #000"> Supported by<br />NSF, DOE, NIH</p> </div> </div> </div> <div class="row" style="color:#FFF; background-color: #669966; padding-top: 3px; padding-bottom: 8px;">  </div> </div> </div> </footer> <script> $.get(function(data){ $("#homequery").typeahead({ source: data, items: 8, minLength: 1, delay: 60, autoSelect: true, }); },'json'); $('#btnSearch').on('click', function () { var url; var searchInput = $('#homequery').val(); //if (searchInput) { url = "solrsearch.html?query=" + searchInput; window.open(url); } //minimum of 3 characters var regex0 = new RegExp ( "(.){3,}" ); var results0 = regex0.exec( searchInput ); if (results0 !== null) { //test for an PDB-IHM id with or without "PDBDEV" prefix var regex1 = new RegExp ( "^[pP][dD][bB][dD][eE][vV]_[0-9]{8,}$" ); var regex2 = new RegExp ( "^[0-9]{8,}$" ); //pure number 8+ digits var results1 = regex1.exec( searchInput ); var results2 = regex2.exec( searchInput ); if (results1 !== null) { url = "entry.html?PDBDEV_" + searchInput.slice(7); window.open(url); } else if (results2 !== null) { url = "entry.html?PDBDEV_" + searchInput; window.open(url); } else { url = "solrsearch.html?query=" + searchInput; window.open(url); } } }); </script> <script> function openAnchorAccordion() { if (window.location.hash) { var jQuerytarget = jQuery('body').find(window.location.hash); if (jQuerytarget.hasClass('collapse')) { var jQuerytargetAccordion = jQuerytarget.find('.collapse'); jQuerytarget.collapse('show'); } } } openAnchorAccordion(); jQuery("body").on("click", "a", openAnchorAccordion); </script> </div> </body> </html>

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