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Henderson R.,University of Cambridge | Sali A.,University of California at San Francisco | Baker M.L.,Baylor College of Medicine | Carragher B.,Scripps Research Institute | And 26 more authors.
Structure | Year: 2012

This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine. © 2012 Elsevier Ltd. All rights reserved.


Lawson C.L.,Rutgers University | Baker M.L.,Baylor College of Medicine | Best C.,Protein Data Bank in Europe | Bi C.,Rutgers University | And 20 more authors.
Nucleic Acids Research | Year: 2011

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. © The Author(s) 2010.


Ludtke S.J.,Baylor College of Medicine | Lawson C.L.,Rutgers University | Kleywegt G.J.,Protein Data Bank in Europe | Berman H.M.,Rutgers University | Chiu W.,Baylor College of Medicine
Pacific Symposium on Biocomputing 2011, PSB 2011 | Year: 2011

Electron cryo-microscopy (cryoEM) is a rapidly maturing methodology in structural biology, which now enables the determination of 3D structures of molecules, macromolecular complexes and cellular components at resolutions as high as 3.5Å, bridging the gap between light microscopy and X-ray crystallography/NMR. In recent years structures of many complex molecular machines have been visualized using this method. Single particle reconstruction, the most widely used technique in cryoEM, has recently demonstrated the capability of producing structures at resolutions approaching those of X-ray crystallography, with over a dozen structures at better than 5 Å resolution published to date. This method represents a significant new source of experimental data for molecular modeling and simulation studies. CryoEM derived maps and models are archived through joint deposition services to the EM Data Bank (EMDB) and Protein Data Bank (PDB), respectively. CryoEM maps are now being routinely produced over the 3-30 Å resolution range, and a number of computational groups are developing software for building coordinate models based on this data and developing validation techniques to better assess map and model accuracy. In this workshop we will present the results of the first cryoEM modeling challenge, in which computational groups were asked to apply their tools to a selected set of published cryoEM structures. We will also compare the results of the various applied methods, and discuss the current state of the art and how we can most productively move forward. © 2011 World Scientific Publishing Co. Pte. Ltd.


Chambers J.,ChEMBL | Davies M.,ChEMBL | Gaulton A.,ChEMBL | Hersey A.,ChEMBL | And 6 more authors.
Journal of Cheminformatics | Year: 2013

UniChem is a freely available compound identifier mapping service on the internet, designed to optimize the efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based resources. In the past, the creation and maintenance of such links at EMBL-EBI, where several chemistry-based resources exist, has required independent efforts by each of the separate teams. These efforts were complicated by the different data models, release schedules, and differing business rules for compound normalization and identifier nomenclature that exist across the organization. UniChem, a large-scale, non-redundant database of Standard nChIs with pointers between these structures and chemical identifiers from all the separate chemistry resources, was developed as a means of efficiently sharing the maintenance overhead of creating these links. Thus, for each source represented in UniChem, all links to and from all other sources are automatically calculated and immediately available for all to use. Updated mappings are immediately available upon loading of new data releases from the sources. Web services in UniChem provide users with a single simple automatable mechanism for maintaining all inks from their resource to all other sources represented in UniChem. In addition, functionality to track changes in identifier usage allows users to monitor which identifiers are current, and which are obsolete. Lastly, UniChem has been deliberately designed to allow additional resources to be included with minimal effort. Indeed, the recent inclusion of data sources external to EMBL-EBI has provided a simple means of providing users with an even wider selection of resources with which to link to, all at no extra cost, while at the same time providing a simple mechanism for external resources to link to all EMBL-EBI chemistry resources. © 2013 Chambers et al.; licensee Chemistry Central Ltd.


EMPIAR provides raw 2-D data for datasets submitted to the EMDB, and is managed by the Protein Data Bank in Europe team at EMBL-EBI. Credit: Spencer Phillips, EMBL-EBI As the bioimaging revolution gives scientists ever-more detailed views on the inner workings of cells, there is growing demand for public infrastructure to store, share and link the massive datasets produced using high-resolution imaging techniques. Complementing large-scale, EMBL-led, intergovernmental initiatives such as Euro-BioImaging, the European Bioinformatics Institute (EMBL-EBI) has expanded its EMPIAR data service to accommodate new high-resolution imaging modalities such as Scanning Electron Microscopy (SEM). A correspondence published in Nature Methods today introduces the resource and gives a glimpse of future developments. EMPIAR, EMBL-EBI's global public data resource for raw 2D images, provides valuable data for developing new approaches to data processing, interpretation and validation - all essential activities for archiving and quality control. "The raw image data archived in EMPIAR is very useful for many things, including making original data related to controversial studies available publicly," explains Gerard Kleywegt, Head of Molecular and Cellular Structure services at EMBL-EBI. EMPIAR, part of the Electron Microscopy Data Bank (EMDB) at EMBL-EBI, is designed to handle very large datasets: the average entry is around 700 Gigabytes, and the largest is over 6 Terabytes. Recent datasets include four related 3D SEM entries showing different stages of infection of a red blood cell by a malaria parasite. EMPIAR is currently the only way to archive these data and make them available to other scientists. "EMPIAR allows us to share big raw datasets," says John Briggs of EMBL, whose group develops and applies advanced cryo-electron microscopy techniques to study enveloped viruses such as HIV. "These can then be looked at by other labs that might be interested in other aspects of the data, or used for testing or comparing new image-analysis pipelines." "EMPIAR is an exemplar of a very timely, community-driven archiving initiative, and fits perfectly with our mission to provide services that support life-science discovery," says EMBL Director General Iain Mattaj. "It supports cutting-edge imaging methods such as those developed at EMBL by giving a home to the data, and allowing the community to refine their interpretation. This enables us to gain an increasingly precise view on the processes of life." The EMPIAR team is working on ways to accommodate other imaging modalities, for example soft X-ray tomography - which bridges the scale and resolution gap between light microscopy and electron tomography - and Correlative Light and Electron Microscopy (CLEM). "In CLEM, researchers use fluorescent tags to detect interesting events in a cell, then take a closer look using high-resolution EM," says Ardan Patwardhan, Coordinator in EMBL-EBI's Protein Data Bank in Europe team. "We are working with pioneers in this field to find the best way to store and correlate these data types, which will provide a very powerful tool for research." More information: Iudin A, et al. (2016) EMPIAR: A public archive for raw electron microscopy image data. Nature Methods. DOI: 10.1038/nmeth.3806


Caboche S.,Protein Data Bank in Europe | Caboche S.,University of Lille Nord de France
Journal of Cheminformatics | Year: 2013

2D diagrams are widely used in the scientific literature to represent interactions between ligands and biomacromolecules. Such schematic diagrams are very helpful to better understand the chemical interactions and biological processes in which ligands are involved. Here, a new tool for automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions is presented. LeView (Ligand-Environment Viewer) produces customised and high-quality figures, with a good compromise between a faithful representation of the 3D data (structures and interactions) and aesthetic criteria. LeView can be freely downloaded at http://www.pegasebiosciences.com/tools/leview/. © 2013 Caboche; licensee Chemistry Central Ltd.


Velankar S.,Protein Data Bank in Europe | Alhroub Y.,Protein Data Bank in Europe | Best C.,Protein Data Bank in Europe | Caboche S.,Protein Data Bank in Europe | And 28 more authors.
Nucleic Acids Research | Year: 2012

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). © The Author(s) 2011.


Velankar S.,Protein Data Bank in Europe | Dana J.M.,Protein Data Bank in Europe | Jacobsen J.,UniProt | Van Ginkel G.,Protein Data Bank in Europe | And 6 more authors.
Nucleic Acids Research | Year: 2013

The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information. © The Author(s) 2012.


Gutmanas A.,Protein Data Bank in Europe | Oldfield T.J.,Protein Data Bank in Europe | Patwardhan A.,Protein Data Bank in Europe | Sen S.,Protein Data Bank in Europe | And 2 more authors.
Acta Crystallographica Section D: Biological Crystallography | Year: 2013

The history and the current state of the PDB and EMDB archives is briefly described, as well as some of the challenges that they face. It seems natural that the role of structural biology archives will change from being a pure repository of historic data into becoming an indispensable resource for the wider biomedical community. As part of this transformation, it will be necessary to validate the biomacromolecular structure data and ensure the highest possible quality for the archive holdings, to combine structural data from different spatial scales into a unified resource and to integrate structural data with functional, genetic and taxonomic data as well as other information available in bioinformatics resources. Some recent developments and plans to address these challenges at PDBe are presented. © 2013 International Union of Crystallography Printed in Singapore - all rights reserved.


Velankar S.,Protein Data Bank in Europe | Alhroub Y.,Protein Data Bank in Europe | Alili A.,Protein Data Bank in Europe | Best C.,Protein Data Bank in Europe | And 29 more authors.
Nucleic Acids Research | Year: 2011

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. © The Author(s) 2010.

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