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Hamilton GL, Alper J, Sanabria H. Reporting on the future of integrative structural biology ORAU workshop. Front Biosci (Landmark Ed) 2020; 25:43-68. [PMID: 31585877 DOI: 10.2741/4794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Integrative and hybrid methods have the potential to bridge long-standing knowledge gaps in structural biology. These methods will have a prominent role in the future of the field as we make advances toward a complete, unified representation of biology that spans the molecular and cellular scales. The Department of Physics and Astronomy at Clemson University hosted The Future of Integrative Structural Biology workshop on April 29, 2017 and partially sponsored by partially sponsored by a program of the Oak Ridge Associated Universities (ORAU). The workshop brought experts from multiple structural biology disciplines together to discuss near-term steps toward the goal of a molecular atlas of the cell. The discussion focused on the types of structural data that should be represented, how this data should be represented, and how the time domain might be incorporated into such an atlas. The consensus was that an explorable, map-like Virtual Cell, containing both spatial and temporal data bridging the atomic and cellular length scales obtained by multiple experimental methods, represents the best path toward a complete atlas of the cell.
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Affiliation(s)
- George L Hamilton
- Physics and Astronomy, Clemson University, 216 Kinard Lab, Clemson, S.C. USA
| | - Joshua Alper
- Physics and Astronomy, Clemson University, 302B Kinard Lab, Clemson, S.C. 29634-0978. USA
| | - Hugo Sanabria
- Physics and Astronomy, Clemson University, 214 Kinard Lab, Clemson, S.C. 29634-0978. USA,
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2
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Ortega DR, Oikonomou CM, Ding HJ, Rees-Lee P, Jensen GJ. ETDB-Caltech: A blockchain-based distributed public database for electron tomography. PLoS One 2019; 14:e0215531. [PMID: 30986271 PMCID: PMC6464211 DOI: 10.1371/journal.pone.0215531] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/03/2019] [Indexed: 01/12/2023] Open
Abstract
Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets.
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Affiliation(s)
- Davi R. Ortega
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Catherine M. Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - H. Jane Ding
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Prudence Rees-Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | | | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Howard Hughes Medical Institute, Pasadena, California, United States of America
- * E-mail:
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3
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Kroon-Batenburg LMJ, Helliwell JR, McMahon B, Terwilliger TC. Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements. IUCRJ 2017; 4:87-99. [PMID: 28250944 PMCID: PMC5331468 DOI: 10.1107/s2052252516018315] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/15/2016] [Indexed: 05/20/2023]
Abstract
A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an 'Open Science' model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education and training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction data via different types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromol-ecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. A number of specific case studies are presented, including an example research thread that provides complete open access to raw data.
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Affiliation(s)
- Loes M. J. Kroon-Batenburg
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, CH 3584, The Netherlands
| | - John R. Helliwell
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
| | - Brian McMahon
- International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, UK
| | - Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507, USA
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4
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Salavert-Torres J, Iudin A, Lagerstedt I, Sanz-García E, Kleywegt GJ, Patwardhan A. Web-based volume slicer for 3D electron-microscopy data from EMDB. J Struct Biol 2016; 194:164-70. [PMID: 26876163 PMCID: PMC4819904 DOI: 10.1016/j.jsb.2016.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 12/05/2022]
Abstract
We describe the functionality and design of the Volume slicer – a web-based slice viewer for EMDB entries. This tool uniquely provides the facility to view slices from 3D EM reconstructions along the three orthogonal axes and to rapidly switch between them and navigate through the volume. We have employed multiple rounds of user-experience testing with members of the EM community to ensure that the interface is easy and intuitive to use and the information provided is relevant. The impetus to develop the Volume slicer has been calls from the EM community to provide web-based interactive visualisation of 2D slice data. This would be useful for quick initial checks of the quality of a reconstruction. Again in response to calls from the community, we plan to further develop the Volume slicer into a fully-fledged Volume browser that provides integrated visualisation of EMDB and PDB entries from the molecular to the cellular scale.
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Affiliation(s)
- José Salavert-Torres
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom; Present address: Universitat Politècnica de València, DISCA, Edificio 1G - Lab 3S-15, Camino de Vera S/N, 46022 València, Spain.
| | - Andrii Iudin
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
| | - Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
| | - Eduardo Sanz-García
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
| | - Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom.
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5
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Abstract
The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.
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Affiliation(s)
- Bart van Beusekom
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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6
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Guss JM, McMahon B. How to make deposition of images a reality. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2520-32. [PMID: 25286838 PMCID: PMC4188000 DOI: 10.1107/s1399004714005185] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 03/06/2014] [Indexed: 11/24/2022]
Abstract
The IUCr Diffraction Data Deposition Working Group is investigating the rationale and policies for routine deposition of diffraction images (and other primary experimental data sets). An information-management framework is described that should inform policy directions, and some of the technical and other issues that need to be addressed in an effort to achieve such a goal are analysed. In the near future, routine data deposition could be encouraged at one of the growing number of institutional repositories that accept data sets or at a generic data-publishing web repository service. To realise all of the potential benefits of depositing diffraction data, specialized archives would be preferable. Funding such an initiative will be challenging.
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Affiliation(s)
- J. Mitchell Guss
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Brian McMahon
- International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
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7
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Patwardhan A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grünewald K, Heriche JK, Koster A, Kühlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-García E, Subramaniam S, Verkade P, Swedlow JR, Kleywegt GJ. A 3D cellular context for the macromolecular world. Nat Struct Mol Biol 2014; 21:841-5. [PMID: 25289590 PMCID: PMC4346196 DOI: 10.1038/nsmb.2897] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community.
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Affiliation(s)
- Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | | | - Sarah Butcher
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Raffaella Carzaniga
- Electron Microscopy Unit, Cancer Research UK London Research Institute, London, UK
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Lucy Collinson
- Electron Microscopy Unit, Cancer Research UK London Research Institute, London, UK
| | - Pascal Doux
- FEI Visualization Sciences Group, Mérignac, France
| | | | - Mark H Ellisman
- Center for Research in Biological Systems, National Center for Microscopy and Imaging Research (NCMIR), University of California, San Diego, San Diego, California, USA
| | - Erik Franken
- FEI Electron Optics B.V., Eindhoven, the Netherlands
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Jean-Karim Heriche
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Abraham Koster
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Carolyn Larabell
- Department of Anatomy, University of California, San Francisco, San Francisco, California, USA
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics, Rutgers University, Piscataway, New Jersey, USA
| | - Helen R Saibil
- Institute of Structural and Molecular Biology, Department of Crystallography, Birkbeck College, London, UK
| | - Eduardo Sanz-García
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Sriram Subramaniam
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Paul Verkade
- Wolfson Bioimaging Facility, School of Biochemistry, University of Bristol, Bristol, UK
| | - Jason R Swedlow
- Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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8
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Vařeková RS, Jaiswal D, Sehnal D, Ionescu CM, Geidl S, Pravda L, Horský V, Wimmerová M, Koča J. MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res 2014; 42:W227-33. [PMID: 24848013 PMCID: PMC4086108 DOI: 10.1093/nar/gku426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Structure validation has become a major issue in the structural biology community, and an essential step is checking the ligand structure. This paper introduces MotiveValidator, a web-based application for the validation of ligands and residues in PDB or PDBx/mmCIF format files provided by the user. Specifically, MotiveValidator is able to evaluate in a straightforward manner whether the ligand or residue being studied has a correct annotation (3-letter code), i.e. if it has the same topology and stereochemistry as the model ligand or residue with this annotation. If not, MotiveValidator explicitly describes the differences. MotiveValidator offers a user-friendly, interactive and platform-independent environment for validating structures obtained by any type of experiment. The results of the validation are presented in both tabular and graphical form, facilitating their interpretation. MotiveValidator can process thousands of ligands or residues in a single validation run that takes no more than a few minutes. MotiveValidator can be used for testing single structures, or the analysis of large sets of ligands or fragments prepared for binding site analysis, docking or virtual screening. MotiveValidator is freely available via the Internet at http://ncbr.muni.cz/MotiveValidator.
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Affiliation(s)
- Radka Svobodová Vařeková
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Deepti Jaiswal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - David Sehnal
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Crina-Maria Ionescu
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislav Geidl
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Lukáš Pravda
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Vladimír Horský
- Faculty of Informatics, Masaryk University Brno, Botanická 68a, 602 00 Brno, Czech Republic
| | - Michaela Wimmerová
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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9
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Abstract
Efforts from the TB Structural Genomics Consortium together with those of tuberculosis structural biologists worldwide have led to the determination of about 350 structures, making up nearly a tenth of the pathogen's proteome. Given that knowledge of protein structures is essential to obtaining a high-resolution understanding of the underlying biology, it is desirable to have a structural view of the entire proteome. Indeed, structure prediction methods have advanced sufficiently to allow structural models of many more proteins to be built based on homology modeling and fold recognition strategies. By means of these approaches, structural models for about 2,877 proteins, making up nearly 70% of the Mycobacterium tuberculosis proteome, are available. Knowledge from bioinformatics has made significant inroads into an improved annotation of the M. tuberculosis genome and in the prediction of key protein players that interact in vital pathways, some of which are unique to the organism. Functional inferences have been made for a large number of proteins based on fold-function associations. More importantly, ligand-binding pockets of the proteins are identified and scanned against a large database, leading to binding site-based ligand associations and hence structure-based function annotation. Near proteome-wide structural models provide a global perspective of the fold distribution in the genome. New insights about the folds that predominate in the genome, as well as the fold combinations that make up multidomain proteins, are also obtained. This chapter describes the structural proteome, functional inferences drawn from it, and its applications in drug discovery.
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10
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Berman HM, Kleywegt GJ, Nakamura H, Markley JL. How community has shaped the Protein Data Bank. Structure 2014; 21:1485-91. [PMID: 24010707 DOI: 10.1016/j.str.2013.07.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/12/2013] [Accepted: 07/17/2013] [Indexed: 11/19/2022]
Abstract
Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules. Since then, the number, size, and complexity of structural models have continued to grow, reflecting the productivity of structural biology. Managed by the Worldwide PDB organization, the PDB has been able to meet increasing demands for the quantity of structural information and of quality. In addition to providing unrestricted access to structural information, the PDB also works to promote data standards and to raise the profile of structural biology with broader audiences. In this perspective, we describe the history of PDB and the many ways in which the community continues to shape the archive.
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Affiliation(s)
- Helen M Berman
- RCSB PDB, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ USA 08854.
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11
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Brooksbank C, Bergman MT, Apweiler R, Birney E, Thornton J. The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res 2014; 42:D18-25. [PMID: 24271396 PMCID: PMC3964968 DOI: 10.1093/nar/gkt1206] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/01/2013] [Accepted: 11/04/2013] [Indexed: 12/18/2022] Open
Abstract
Molecular Biology has been at the heart of the 'big data' revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of Dayhoff's 'Atlas of Protein Sequence and Structure' through the Human Genome Project in the late 1990s and early 2000s to today's population-scale sequencing initiatives. The European Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.uk) is one of three organizations worldwide that provides free access to comprehensive, integrated molecular data sets. Here, we summarize the principles underpinning the development of these public resources and provide an overview of EMBL-EBI's database collection to complement the reviews of individual databases provided elsewhere in this issue.
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Affiliation(s)
- Catherine Brooksbank
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mary Todd Bergman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Rolf Apweiler
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Janet Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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12
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Gutmanas A, Alhroub Y, Battle GM, Berrisford JM, Bochet E, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Gore SP, Haslam P, Hatherley R, Hendrickx PMS, Hirshberg M, Lagerstedt I, Mir S, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley RA, Velankar S, Wainwright ME, Kleywegt GJ. PDBe: Protein Data Bank in Europe. Nucleic Acids Res 2013; 42:D285-91. [PMID: 24288376 PMCID: PMC3965016 DOI: 10.1093/nar/gkt1180] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Protein Data Bank in Europe (pdbe.org) is a founding member of the Worldwide PDB consortium (wwPDB; wwpdb.org) and as such is actively engaged in the deposition, annotation, remediation and dissemination of macromolecular structure data through the single global archive for such data, the PDB. Similarly, PDBe is a member of the EMDataBank organisation (emdatabank.org), which manages the EMDB archive for electron microscopy data. PDBe also develops tools that help the biomedical science community to make effective use of the data in the PDB and EMDB for their research. Here we describe new or improved services, including updated SIFTS mappings to other bioinformatics resources, a new browser for the PDB archive based on Gene Ontology (GO) annotation, updates to the analysis of Nuclear Magnetic Resonance-derived structures, redesigned search and browse interfaces, and new or updated visualisation and validation tools for EMDB entries.
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Affiliation(s)
- Aleksandras Gutmanas
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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13
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Morris C. Towards a structural biology work bench. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:681-2. [PMID: 23633576 PMCID: PMC3640465 DOI: 10.1107/s090744491300276x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/07/2013] [Indexed: 11/25/2022]
Abstract
The trends to investigate larger complexes and more transient phenomena pose some challenges to software developers. This is an introduction to four papers based on presentations given at a workshop entitled Integrated Software for Integrative Structural Biology. The use of hybrid techniques, and other trends in structural research, pose new challenges to software developers. A structural biology work bench that meets these needs would provide seamless data transfer between processing steps, and accumulate archival data and metadata without intruding into the scientist’s work process.
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