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June 25, 2024: A paper co-authored by all organizers and participants in the EMDataResource Ligand Challenge has now been published in Nature Methods. The paper describes the results of our 2021 Challenge and recommends best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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A workshop was held at EMBL-EBI (Hinxton, UK) in January 2020 to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis and setting community recommendations.
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A new publication in the NAR Database issue entitled "EMDB--The Electron Microscopy Data Bank" addresses the recent developments in the archiving of 3DEM data and the future plans for the EMDB.
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wwPDB is excited to announce that Kyle Morris has joined the EMDB team as their new team leader. Kyle brings 10 years of experience in the cryo-EM field.
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Starting September 23, wwPDB validation of 3DEM structures for which there is both a model and an EM volume will include the Q-score metric
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A new time-saving EM-specific template for metadata input is now available at the PDB_EXTRACT website. The template eases the burden of depositing multiple related structures to the wwPDB OneDep System.
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EMDR has a new web service for validation of RNA structures determined using cryo-EM and other experimental methods. RNA adopts complex three-dimensional folding patterns in biology such as ribosomal particles, spliceosomes, RNA viruses, and polymerase complexes.
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From February 25, 2022, deposition of half-maps for single-particle, single-particle-based helical, and sub-tomogram averaging reconstructions to the EM Data Bank (EMDB) will become mandatory.
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From February 9, 2022, the wwPDB EMDB Core Archive will exclusively support version 3 of its data model and retire version 1.9.6 header files from the archive.
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February 4, 2021: The final version of the paper describing the outcomes of the 2019 Model Metrics Challenge is now published in Nature Methods with an accompanying News & Views commentary.
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February 1, 2021: Our next model challenge launches today: the 2021 EMDataResource Ligand Model Challenge. The task for modeler teams in this round is to optimize reference models against selected target maps containing protein or protein+RNA, ligands, ions and solvent (1.9-2.5 Å resolution range).
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The wwPDB archive has now been updated to include validation reports for every released set of EM model coordinates in the PDB and every released EMDB map entry. Validation reports provide quantitative and visual assessments of structure quality and enable archive-wide comparisons.
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In 2020 we made several important enhancements to the EMDR website to better enable our visitors to quickly find and view summary information about their map entries of interest.
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Following ground-breaking developments in 2018, CASP (Critical Assessment of protein Structure Prediction) will present another round of exciting progress in the field via virtual conference Nov 30-Dec 4, 2020.
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A 3-day virtual/online meeting "Cryo-EM Validation in the Age of SARS-CoV-2: Methods, Tools and Applications" (Nov 18-20) will present current thinking on cryo-EM map and map/model validation, and consider future research directions.
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Sept-2020: Updated validation reports for all X-ray, NMR, and 3DEM structures released in the PDB archive are now available. Of particular importance for cryo-EM, the updated report format includes EM map analysis, and fit of EM model to its map volume. FSC curves are also included to compare reported and estimated resolution, where either half maps or FSC data was uploaded.
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June 15 2020:"Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution" is available as a preprint at BioRxiv while under consideration for publication.
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The 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP) round started on May 18, 2020.
Membrane proteins and protein complexes are particularly needed.
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Beginning April 15 2020, the Electron Microscopy Data Bank (EMDB) will end its practice of releasing map entry metadata (so-called XML header files) prior to release of the primary map and associated files.
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1 April 2020: To aid COVID-19-related research efforts, we provide here several coronavirus(CoV)-related resources and links, including a new enhanced search for CoV-related maps, and movies comparing SARS spike trimers.
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5 February 2020: Congratulations are in order to the cryo-EM community for reaching a significant new milestone: more than 10,000 maps representing a wide variety of biological assemblies are now available in the EM Data Bank archive.
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A publication by members of the EMDR team describing the history of developing data standards for Cryo-EM methods is now available online via the journal Structural Dynamics.
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To ensure consistent and coherent rules for EMDB data processing, a comprehensive policy and procedures document has been drawn up for the EMDB and is now available to view on the EMDB website.
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Time-stamped snapshots of the PDB and EMDB archives are available as of January 1, 2020.
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Validation reports provided in the wwPDB OneDep system now have additional validation for EM maps to help users identify potential discrepancies in their data. EMDataResource played a key role in development of these new features.
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Versioning now allows depositors to update their coordinates while retaining the same PDB accession code.
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The Workshop on Biological Structure Determination using Cryo-EM was held on July 22-23, 2019 as part of the American Crystallographic Association Annual Meeting in Covington, Kentucky USA. Materials for the workshop can be accessed via this post.
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EMDataResource is trying something new and has put together a smaller, shorter-timeline EM model challenge. The deadline for submission of completed models fitted to target maps (2-3 Å resolution range) is May 25 May 28 (3 PM US Eastern).
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The allocation of 4 digits for EMDB accession codes will soon come to an end. New EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted.
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The EMDataBank/Unified Data Resource for 3DEM Project, established in 2007 to serve the scientific community as a global portal for deposition, search, services, and events rel
ated to 3D (cryo) electron microscopy, has a new name: EMDataResource. This name change more clearly distinguishes our collaborative project from the EMDB Map
Data Archive.
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"The CryoEM Map and Model Structure Challenges," a thematic collection of 18 peer-reviewed articles plus editorial being published in the Journal of Structural Biology, is now available online.
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The Cryo-EM Workshop: A Guide to High Resolution Structure Determination was held on July 21, 2018 as part of the ACA Annual Meeting in Toronto. Materials from the workshop can be accessed through the links below.
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The wwPDB OneDep system will require contact authors to provide their unique ORCID identifiers later this summer.
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The new version of OneDep improves the process of data replacement for PDB and EMDB entries, prior to their release. In addition, we have udpated the wwPDB privacy policy.
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Due to rapid growth, EMDB is running out of 4 digit accession codes. Going forward, EMDB accession codes will have a variable format for their numerical portion.
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Critical Assessment of Techniques for Protein Structure Prediction (CASP) community experiments aim to advance the state of the art in protein structure modeling. The thirteenth CASP round is scheduled to start on May 1, 2018. The organizing committee is particularly keen to include cryo-EM-derived structure targets in this round.
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In collaboration with the Journal of Structural Biology we are in the process of producing a special issue on the 2016 Map and Model Challenges,
with Wah Chiu and Cathy Lawson serving as the guest editors.
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Congratulations to Jacques Dubochet, Joachim Frank, and Richard
Henderson, who have received the 2017 Nobel Prize in Chemistry for
developing cryo-electron microscopy, a technique that allows scientists to visualize the structural details of biological molecules and gain
insights into how living systems function.
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In 2016 EMDataBank (now EMDataResource) ran two community challenges in parallel to create awareness of the need for cryoEM structure validation as a routine process in research studies and publications, and to expedite development of quantitative tools for assessment. The Map and Model Challenges were developed by cryoEM and modeling community experts, respectively, who have been charged with developing challenge tasks, promoting worldwide participation, evaluating the results, and producing a report.
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The wwPDB is planning to introduce in 2017 a new procedure for the management by the Depositor of Record (where the Depositor of Record is defined as the Principal Investigator for the entry) of substantial revisions to previously released PDB archival entries.
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On July 12, 2017, the wwPDB partners plan to update the PDB FTP archive with PDB structure entry files conforming to V5.0 of the PDBx/mmCIF dictionary, which already supports the global wwPDB system for Deposition, Biocuration, and Validation of PDB data - OneDep.
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As part of the Proceedings of the CCP-EM Spring Symposium, Ardan Patawardhan (PDBe) provides an overview of trends affecting the field of cryo-EM, making use of data available in the EMDB archive. Have a look here.
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The paper describing wwPDB OneDep system is now available. The wwPDB has deployed a unified system for deposition, biocuration, and validation of macromolecular structures globally across all wwPDB, EMDB, and BMRB deposition sites to meet the evolving requirements of the scientific community to archive structural data over the coming decades.
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19 January 2017: This week, a delegation from the Society of Chinese Cryo Electron Microscopy (SCCEM) visited EMBL-EBI to discuss how cryo-EM data in EMDB and EMPIAR could be made available to users from within China.
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The wwPDB and the EMDataBank/Unified Data Resource for 3DEM Project have collaborated to update the experimental methods descriptions of all electron microscopy and electron crystallography-derived structures in the PDB archive. With this work now completed, all 3DEM-derived entries have better-organized content and conform to the revised data model developed by our team for use within the wwPDB OneDep System.
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The Assessment Phase of the Map Challenge is now officially open, and all are welcome to participate. The Challenge Phase (July 2015-Apr 2016) was a tremendous success, with 66 submitted maps spread across the 7 image data benchmark targets.
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The wwPDB and the Unified Data Resource for 3DEM Project (https://www.ncbi.nlm.nih.gov/pubmed/26578576) are collaborating to update the experimental methods descriptions of all electron microscopy and electron crystallography-derived structures in the PDB archive.
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The new wwPDB Validation Server at https://validate.wwpdb.org now generates preliminary validation reports for structures solved by NMR and 3D Electron Microscopy, in addition to X-ray crystallography.
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Effective September 6th, 2016, deposition to the PDB of atomic models determined by 3D Electron cryo-Microscopy (3DEM) will require prior or simultaneous deposition of the associated 3DEM volume maps to EMDB.
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The wwPDB Partners and our team are pleased to announce that validation reports for all Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) structures already represented in the global PDB archive have been publicly released.
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Starting May 31st 2016, the legacy deposition systems EMDep, AutoDep, and EM-ADIT will no longer accept new EMDB and PDB submissions. Depositors with in-progress sessions on the legacy systems will be able to access and complete their deposition sessions until September 30th 2016.
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The wwPDB Partners and our team are pleased to announce that validation reports for all Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) structures already represented in the global PDB archive will become publicly available in May.
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The second International Conference on Image Analysis in Three-dimensional Cryo-EM, will be held at Granlibakken Conference Center, Lake Tahoe, California from March 30 to April 2, 2016. The second workshop in this series will again focus on cutting edge techniques for image analysis in Cryo-EM.
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The wwPDB partners and our team are pleased to announce the launch of a new Deposition & Annotation system that supports structures determined using 3DEM, NMR, and X-ray, neutron and electron crystallography.
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New open access articles about our project and EMDB access are now available online, in advance of publication in the upcoming January 2016 Nucleic Acids Research Database Issue.
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Nov 9, 2015: We have two major announcements regarding the ongoing Map Challenge.
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All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors.
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All members of the Scientific Community--at all levels of experience--are invited to participate as Challengers, and/or as Assessors.
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EMPIAR (Electron Microscopy Pilot Image ARchive; http://pdbe.org/empiar) is a public archive for raw image data (micrographs, particles, and tilt-series) related to EMDB entries. Important uses of EMPIAR data include validation and as test-data for methods development and teaching.
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The PDBe tilt-pair validation web-server is now available from: http://www.pdbe.org/tiltpair. You can use this service to perform a tilt-pair analysis on your own data.
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The EMDB team at the Protein Data Bank in Europe (PDBe) has two vacancies for scientific programmers to work on an exciting new MRC and BBSRC funded project to help bridge the worlds of cellular and molecular structural biology.
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June 2014: Our Partner PDBe was recently awarded funding by MRC and BBSRC to set up a public archive for raw image data (micrographs, particles, and tilt-series) related to EMDB entries. The archive currently contains 7 datasets related to EMDB map entries, including a few multi-frame direct electron detector datasets.
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Our Partner PDBe (EBI) and their collaborators at the Science & Technology Facilities Council in Daresbury are developing a web service as part of the BioMedBridges project that will enable the EMDB and PDB archives to be searched on the basis of 3D volumetric shape matching, rather than solely on the basis of metadata and/or coordinate models. The PDBe/STFC Biomedbridges team requests your input on 3D volume segmentation, which in many cases will be a necessary step before volume matching.
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A record number of EM structural data entries were released in 2013: 544 EMDB maps, and 236 EM-PDB models. The overall size of the EM structural data archives has also substantially increased.
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The first International Conference on Image Analysis in Three-dimensional Cryo-EM, to be held at Granlibakken Conference Center, Lake Tahoe, California from March 12 to March 15, 2014. The goal of the Symposium is to discuss state of the art image analysis approaches to tackle challenging biological problems and to identify current limitations and remaining problems in the field as currently practiced.
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Recent improvements to web-based visualisation and analysis of 3DEM data from EMDB and PDB are described in an open access article published in the November issue of the Journal of Structural Biology.
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We have created a short online poll to collect your opinions about a possible change to EMDB data release policy. Should complete experimental metadata associated with EMDB map entries continue to be available/searchable prior to map release?
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The use of 3D cryo-electron microscopy reconstruction (3DEM) methods to experimentally determine structures of biological macromolecules, complexes and machines is rapidly increasing in the structural biology community. For journal articles reporting new 3DEM structures via single particle, helical, electron crystallography, and sub-tomogram averaging methods, we find that the overall map-deposition rate to EM Data Bank (EMDB) is approaching 70%. However, the rate varies significantly per journal, and tends to be highest for journals with well-defined and consistently enforced 3DEM deposition policies in place.
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In order to meet the challenges of ever greater numbers of PDB depositions, involving ever larger and more complex structures, often determined using multiple methods, the Worldwide Protein Data Bank partners (wwPDB; http://wwpdb.org/) are developing a completely new system for deposition and annotation of PDB entries.
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On 16 January 2013, the EMDB archive plans to adopt an updated format, v.1.9.0, for the entry header file (XML file associated with each map). This means that EMDB header files distributed from wwPDB partner sites will conform to the 1.9.0 format, and our deposition/annotation/search services will start using this format.
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As we announced early in the year, the EMDB map archive is now distributed alongside the PDB archive by all three wwPDB partner sites. To download or retrieve EMDB map or header files, please go to one of the three current distribution sites.
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The September 2012 special issue of Biopolymers "2010 Cryo-EM Modeling Challenge" is now online. The issue contents include an editorial and eight articles describing results from the 2010 cryo-EM modeling challenge.
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Every now and then depositors of EM data approach us with questions (or gripes) about the deposition process, in particular when both a map and a model are to be deposited.
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Tomographic data deposition was the main topic of an informal afternoon meeting at the 2012 3DEM GRC that drew ~20 conferees.
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A new MRC Partnership grant to provide computational support for UK scientists using electron cryo-microscopy for structural biology will aim to create a new Collaborative Computational Project, CCP-EM. Two excellent, motivated computational scientists are sought to support the Partnership grant and CCP-EM project. For details please view the full announcement here.
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7-March-2012: The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, has joined the PDB archive (https://files.wwpdb.org), as announced previously.
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We are pleased to announce the publication of the outcome of the first Electron Microscopy Validation Task Force (EM VTF) meeting in the journal Structure: Henderson et al., Structure (2012).
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The 6th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods will be held March 14-18, 2012 in Lake Tahoe, CA.
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The EM Data Bank (EMDB), the primary archive for experimentally-determined maps obtained using three-dimensional electron microscopy methods, will join the PDB archive on 7 March 2012.
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We are pleased to announce improved 3D web-based viewing of maps and associated coordinate models from our atlas pages. The molecular visualization program OpenAstexViewer has been adapted by the our team to display EM maps and their associated coordinate models.
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In October 2011, the Worldwide Protein Data Bank (wwPDB) will host a scientific symposium celebrating the 40th anniversary of the inception of the PDB, and the many scientific contributions it archives. The program will showcase the scientific impact made by structural biology during the past 40 years with a distinguished panel of scientists who have been instrumental in the development of the PDB and structural biology.
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A special issue of Biopolymers will cover the results of the first Cryo-EM Modeling Challenge held in 2010 with accompanying workshop at PSB 2011. The challenge was very successful with 136 models submitted by 10 different research groups using 13 different software packages.
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February 2011: Congratulations are in order to the cryoEM community for reaching a significant milestone: more than 1000 maps representing a wide variety of biological assemblies are now archived in the EM DataBank.
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Effective January 2011, the option to hold EM map volumes for two years before release to the public will no longer be available.
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Up-to-date information about our project including history, current status, and future plans can be found in two publications now available online and in press.
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September 2010: We are pleased to announce that a more uniform set of maps is now available through our search services and ftp mirror sites.
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July 2010: The Protein Data Bank in Europe (PDBe; pdbe.org) has a vacancy for the Project Leader Electron Microscopy position.
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2010 Cryo-EM Modeling Challenge and PSB 2011 workshop organized by Steven Ludtke, Wah Chiu, Helen Berman and Gerard Kleywegt.
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June 2010: The EmDataBank.org team is nearing completion of a major project to improve uniformity, viewability and useability of the 730+ map volumes in the EMDB that are currently available for download. Please read on to learn more about this project, and how to access the remediated maps.
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You may have noticed that this site is updated on a weekly basis. EMDB's weekly release cycle is also now synchronized with wwPDB's release cycle.
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You have a brand new cryoEM density map of a biological assembly and want to generate a realistic coordinate model that fits the density. How should you proceed? This was the primary topic of discussion at the Modelling of CryoEM maps workshop held at the University of Houston on January 14-18, 2010.
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The Workshop on Advanced Topics in EM Structure Determination: Challenging Molecules held Nov 8-13, 2009 at the National Resource for Automated Molecular Microscopy (NRAMM) at the Scripps Research Institute, was an intellectually stimulating meeting with over 100 attendees and an outstanding set of instructors. The meeting featured extensive discussion of challenges faced using cryoEM to solve macromolecules that are either small or conformationally variable in structure...
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7 October 2009: This morning, the recipients of the 2009 Nobel Prize for Chemistry were announced. V. Ramakrishnan, T. A. Steitz, and A. E. Yonath will share the award for their studies on the structure and function of the ribosome.
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Christoph Best (PDBe) gave a presentation on how to deposit and retrieve data sets in the EMDB at the 10-day EMBO Course in Cryo-Electron Microscopy at Birkbeck College, London organized by Elena Orlova and Helen Saibil.
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The 2009 3DEM Gordon Research Conference in New London, NH was an exciting meeting with a full roster of excellent presentations and ample time for informal discussions. Team members Christoph Best (PDBe) and Cathy Lawson (RCSB-PDB) presented a poster describing recent progress towards creating a unified data resource for cryoEM.
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March 2009: We are pleased to announce improvements to EM Databank deposition and retrieval services hosted by PDBe (Europe) and RCSB PDB (USA).
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An open access article published in the August 2008 issue of Acta Crystallographica Section D describes the new scheme used by the PDB to archive regular non-crystallographic symmetry information for large biological assemblies.
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Feb 2008: Electron microscopy map data can now be deposited to the EMDB using the improved web-based tool EmDep2.
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Jan 2008: An informal one day workshop organized by Wah Chiu and Cathy Lawson was held on Jan 15, 2008 at the UCSF Mission Bay Campus.
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Aug 2007: An NIH/NIGMS-funded collaboration to create a unified data resource for large complexes determined by cryo-electron microscopy has been established between the Macromolecular Structure Database Group at the European Bioinformatics Institute, the Research Collaboratory for Structural Bioinformatics at Rutgers, and the National Center for Macromolecular Imaging at Baylor College of Medicine.
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In order to develop a community data resource, it is necessary to solicit input from representative members of the scientific community. Below is a summary of past workshops devoted to exchange of cryoEM data that have been organized by members of our project group and other leaders in cryoEM.
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