For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
33
views
52
references
 Top references
cited by
116
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      140
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      EMDataBank unified data resource for 3DEM

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata ( emdatabank.org). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data.

          Related collections

          Most cited references52

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data

          Helen Berman, Kim Henrick, Haruki Nakamura … (2006)
          The worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for more than 38 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The founding members of the wwPDB are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan) [H.M. Berman, K. Henrick and H. Nakamura (2003) Nature Struct. Biol., 10, 980]. The BMRB group (USA) joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Additionally, the wwPDB provides a variety of services to a broad community of users. The wwPDB website at provides information about services provided by the individual member organizations and about projects undertaken by the wwPDB.
          Article 0 comments Cited 369 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            Biochemistry. The resolution revolution.

            W Kühlbrandt (2014)
            Article 0 comments Cited 369 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              How cryo-EM is revolutionizing structural biology.

              Xiao-chen Bai, Greg McMullan, Sjors H W Scheres (2015)
              For many years, structure determination of biological macromolecules by cryo-electron microscopy (cryo-EM) was limited to large complexes or low-resolution models. With recent advances in electron detection and image processing, the resolution by cryo-EM is now beginning to rival X-ray crystallography. A new generation of electron detectors record images with unprecedented quality, while new image-processing tools correct for sample movements and classify images according to different structural states. Combined, these advances yield density maps with sufficient detail to deduce the atomic structure for a range of specimens. Here, we review the recent advances and illustrate the exciting new opportunities that they offer to structural biology research.
              Article 0 comments Cited 270 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (hwp): nar
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 04 January 2016
                Publication date (Electronic): 17 November 2015
                Publication date PMC-release: 17 November 2015
                Volume: 44
                Issue: Database issue , Database issue
                Pages: D396-D403
                Affiliations
                [1 ]Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
                [2 ]Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                [3 ]Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
                Author notes
                [* ]To whom correspondence should be addressed. Tel: +1 848 445 5494; Fax: +1 732 445 4320; Email: cathy.lawson@ 123456rutgers.edu
                Correspondence may also be addressed to Ardan Patwardhan. Tel: +44 1223 492649; Email: ardan@ 123456ebi.ac.uk
                Correspondence may also be addressed to Wah Chiu. Tel: +1 713 798 6985; Fax: +1 713 798 8682; Email: wah@ 123456bcm.edu
                Article
                DOI: 10.1093/nar/gkv1126
                PMC ID: 4702818
                PubMed ID: 26578576
                SO-VID: 4159bf77-9832-4191-815a-cee79dab0c55
                Copyright © © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date accepted : 15 October 2015
                Date received : 01 October 2015
                Page count
                Pages: 8
                Categories
                Subject: Database Issue
                Custom metadata
                cover-date 04 January 2016

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

                Comments

                Comment on this article

                scite_

                Similar content140

                See all similar

                Cited by112

                See all cited by

                Most referenced authors713

                See all reference authors