[Show abstract][Hide abstract] ABSTRACT: The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tools were designed to help non-experts and experts alike to get some insight into the content and assess the quality of 3DEM structures in EMDB and PDB without the need to install specialised software or to download large amounts of data from these archives. The technical challenges encountered in developing these tools, as well as the more general considerations when making archived data available to the user community through a web interface, are discussed.
Full-text · Article · Oct 2013 · Journal of Structural Biology
[Show abstract][Hide abstract] ABSTRACT: Data-intensive research depends on tools that manage multidimensional, heterogeneous datasets. We built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices and tables. OMERO's design and flexibility have enabled its use for light-microscopy, high-content-screening, electron-microscopy and even non-image-genotype data. OMERO is open-source software, available at http://openmicroscopy.org/.
[Show abstract][Hide abstract] ABSTRACT: The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner in the Worldwide PDB organization (wwPDB; wwpdb.org) and as such actively involved in managing the single global archive of biomacromolecular structure data, the PDB. In addition,
PDBe develops tools, services and resources to make structure-related data more accessible to the biomedical community. Here
we describe recently developed, extended or improved services, including an animated structure-presentation widget (PDBportfolio),
a widget to graphically display the coverage of any UniProt sequence in the PDB (UniPDB), chemistry- and taxonomy-based PDB-archive
browsers (PDBeXplore), and a tool for interactive visualization of NMR structures, corresponding experimental data as well
as validation and analysis results (Vivaldi).
Full-text · Article · Nov 2011 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular
structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; wwpdb.org). PDBe also develops new tools
to make structural data more widely and more easily available to the biomedical community. PDBe has developed a browser to
access and analyze the structural archive using classification systems that are familiar to chemists and biologists. The PDBe
web pages that describe individual PDB entries have been enhanced through the introduction of plain-English summary pages
and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures
determined by means of NMR spectroscopy has been expanded. Finally, the entire web site has been redesigned to make it substantially
easier to use for expert and novice users alike. PDBe works closely with other teams at the European Bioinformatics Institute
(EBI) and in the international scientific community to develop new resources with value-added information. The SIFTS initiative
is an example of such a collaboration—it provides extensive mapping data between proteins whose structures are available from
the PDB and a host of other biomedical databases. SIFTS is widely used by major bioinformatics resources.
Full-text · Article · Nov 2010 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and
macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory
for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global ‘one-stop shop’
resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to
the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates
use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.
Full-text · Article · Oct 2010 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: The Protein Data Bank in Europe (PDBe) (http://www.ebi.ac.uk/pdbe/) is actively working with its Worldwide Protein Data Bank partners to enhance the quality and consistency of the international
archive of bio-macromolecular structure data, the Protein Data Bank (PDB). PDBe also works closely with its collaborators
at the European Bioinformatics Institute and the scientific community around the world to enhance its databases and services
by adding curated and actively maintained derived data to the existing structural data in the PDB. We have developed a new
database infrastructure based on the remediated PDB archive data and a specially designed database for storing information
on interactions between proteins and bound molecules. The group has developed new services that allow users to carry out simple
textual queries or more complex 3D structure-based queries. The newly designed ‘PDBeView Atlas pages’ provide an overview
of an individual PDB entry in a user-friendly layout and serve as a starting point to further explore the information available
in the PDBe database. PDBe’s active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and
cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.
Full-text · Article · Jan 2010 · Nucleic Acids Research
[Show abstract][Hide abstract] ABSTRACT: The Electron Microscopy Data Bank (EMDB)  is the global repository for the Internet retrieval of high-resolution three-dimensional images of macromolecular complexes and subcellular structures. Established in 2002 at the European Bioinformatics Institute (EBI), it is now an international effort of EBI, Rutgers University (RCSB) in New Jersey, and the National Center for Macromolecular Imaging (NCMI) in Houston. Deposition of content is rapidly growing as molecular imaging technologies gain widespread use in biological and medical research. Global reuse of these images is a force multiplier by allowing a greater number of scientists access to crucial imagery, thereby furthering science and medicine for the benefit of society. Preserving this 3D imagery for scientists poses special problems that are exemplary of future archival challenges for any kind of digital content management: 1. Governance of criteria for the curation, quality, and protection of this imagery. 2. Creation of the repository infrastructure for these unusual and vital datasets. 3. Establishment and integration of technology and standards to reinforce long-term preservation. 4. Promotion of the repository to achieve wider public use through the Internet. Described are the background, intended impact, scope of content, methods of access, and management of the EMDB repository.