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References

  1. Adams P D Aertgeerts K Bauer C Bell J A Berman H M Bhat T N Blaney J M Bolton E Bricogne G Brown D Burley S K Case D A Clark K L Darden T Emsley P Feher V A Feng Z Groom C R Harris S F Hendle J Holder T Joachimiak A Kleywegt G J Krojer T Marcotrigiano J Mark A E Markley J L Miller M Minor W Montelione G T Murshudov G Nakagawa A Nakamura H Nicholls A Nicklaus M Nolte R T Padyana A K Peishoff C E Pieniazek S Read R J Shao C Sheriff S Smart O Soisson S Spurlino J Stouch T Svobodova R Tempel W Terwilliger T C Tronrud D Velankar S Ward S C Warren G L Westbrook J D Williams P Yang H Young J Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop Structure 2016 24 4 502 508 10.1016/j.str.2016.02.017
  2. Allen F H Bergerhoff G Sievers R Crystallographic Databases 1987 Chester, UK International Union of Crystallography
  3. Allen F H Glusker J P Preface to Special Issue on Crystallographic Databases Acta Crystallogr 2002 B58 3 10.1107/S0108768102006638 unnumbered pages. Also published as Acta Crystallogr, D58(6): unnumbered pages. DOI: https://doi.org/10.1107/S0907444902008399
  4. Aroyo M I Perez-Mato J M Capillas C Kroumova E Ivantchev S Madariaga G Kirov A Wondratschek H Bilbao Crystallographic Server: I. Databases and crystallographic computing programs Z. Kristallogr 2009 221 15 27 10.1524/zkri.2006.221.1.15
  5. Belsky A Hellenbrandt M Karen V L Luksch P New developments in the Inorganic Crystal Structure Database (ICSD): accessibility in support of materials research and design Acta Crystallogr 2002 B58 364 369 10.1107/S0108768102006948
  6. Berman H Kleywegt G Nakamura H Markley J The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future Structure 2012 20 391 396 10.1016/j.str.2012.01.010
  7. Berman H M Henrick K Nakamura H Announcing the worldwide Protein Data Bank Nature Structural Biology 2003 10 980 10.1038/nsb1203-980
  8. Berman H M Westbrook J Feng Z Gilliland G Bhat T N Weissig H Shindyalov I N Bourne P E The Protein Data Bank Nucleic Acids Res 2000 28 1 235 242 10.1093/nar/28.1.235
  9. Berners-Lee T Cool URIs don’t change 1998 Available at: https://www.w3.org/Provider/Style/URI.html [Last accessed 10 April 2017]
  10. Berners-Lee T Fielding R Masinter L Uniform Resource Identifier (URI): Generic Syntax 2005 Available at: https://tools.ietf.org/html/rfc3986 [Last accessed 10 April 2017]
  11. Bernstein H J Bollinger J C Brown I D Gražulis S Hester J R McMahon B Spadaccini N Westbrook J D Westrip S P Specification of the Crystallographic Information File format, version 2.0 Journal of Applied Crystallography 2016 49 277 284 10.1107/S1600576715021871
  12. Codd E F A Relational Model of Data for Large Shared Data Banks Communications of the ACM 1970 13 6 377 387 10.1145/362384.362685
  13. Collins-Sussman B Fitzpatrick B W Pilato C M Version Control with Subversion 2011 Available at: http://svnbook.red-bean.com/en/1.7/svn-book.html [Last accessed 10 April 2017]
  14. Davie P Agbenyega J Collaboration between the CCDC and the IUCr Streamlines Crystallographic Data Deposition into the Cambridge Structural Database 2015 Available at: https://www.ccdc.cam.ac.uk/News/List/post-40/ [Last accessed 10 April 2017]
  15. Davie P Burley S K The Cambridge Crystallographic Data Centre establishes US operations in new partnership with the Rutgers University Center for Integrative Proteomics Research 2013 Available at: https://www.ccdc.cam.ac.uk/News/List/post-25 [Last accessed 10 April 2017]
  16. Davie P Mueller H Alliance Reshapes Crystallography Data Access 2017 Available at: https://www.ccdc.cam.ac.uk/News/List/2017-03-27-alliance-reshapes-crystallography-data-access [Last accessed 10 April 2017]
  17. Day A Linking 2D RSC ChemSpider Compounds to 3D CCDC Crystals 2014 Available at: http://www.rsc.org/blogs/escience/2014/12/linking-2-d-rsc-chemspider-compounds-3-d-ccdc-crystals [Last accessed 10 April 2017]
  18. Day N Downing J Adams S England N W Murray-Rust P CrystalEye: automated aggregation, semantification and dissemination of the world’s open crystallographic data Journal of Applied Crystallography 2012 45 316 323 10.1107/S0021889812006462
  19. Dillo I Hodson S de Waard A (RDA-WDS Interest Group on Income Streams for Data Repositories) Income Streams for Data Repositories Zenodo 2016 10.5281/zenodo.46693
  20. Downs R T Hall-Wallace M The American Mineralogist Crystal Structure Database Am. Mineral 2003 88 247 250
  21. European Synchrotron Radiation Facility ESRF takes the helm in saving data 2016 Available at: http://www.esrf.eu/fr/home/news/general/content-news/general/esrf-takes-the-helm-in-saving-data.html [Last accessed 10 April 2017]
  22. Faber J Fawcett T The Powder Diffraction File: present and future Acta Crystallographica Section B: Structural Science 2002 58 325 332 10.1107/S0108768102003312
  23. First E L Floudas C A MOFomics: Computational pore characterization of metal–organic frameworks Microporous and Mesoporous Materials 2013 165 32 39 10.1016/j.micromeso.2012.07.049
  24. Force11 The FAIR data principles 2014 Available at: https://www.force11.org/group/fairgroup/fairprinciples [Last accessed 10 April 2017]
  25. Galek P T A Pidcock E Wood P A Feeder N Allen F H Navigating the Solid Form Landscape with Structural Informatics Computational Pharmaceutical Solid State Chemistry 2016 Hoboken, NJ John Wiley & Sons, Inc. 15 35 10.1002/9781118700686.ch2
  26. Gallego S V Perez-Mato J M Elcoro L Tasci E S Hanson R M Momma K Aroyo M I Madariaga G MAGNDATA: towards a database of magnetic structures. I. The commensurate case J. Appl. Cryst 2016 49 1750 1776 10.1107/S1600576716012863
  27. Genova F Arviset C Almas B M Bartolo L Broeder D Law E McMahon B Building a Disciplinary, World-Wide Data Infrastructure Data Science J 2017 16 16 10.5334/dsj-2017-016
  28. Goodsell D S Dutta S Zardecki C Voigt M Berman H M Burley S K The RCSB PDB ‘Molecule of the Month’: Inspiring a Molecular View of Biology PLoS Biol 2015 13 e1002140 10.1371/journal.pbio.1002140
  29. Grabowski M Langner K M Cymborowski M Porebski P J Sroka P Zheng H Cooper D R Zimmerman M D Elsliger M-A Burley S K Minor W A public database of macromolecular diffraction experiments Acta Crystallogr 2016 D72 1181 1193 10.1107/S2059798316014716
  30. Gražulis S Chateigner D Downs R T Yokochi A F T Quirós M Lutterotti L Manakova E Butkus J Moeck P Le Bail A Crystallography Open Database – an open-access collection of crystal structures Journal of Applied Crystallography 2009 42 726 729 10.1107/S0021889809016690
  31. Gražulis S Daškevič A Merkys A Chateigner D Lutterotti L Quirós M Serebryanaya N R Moeck P Downs R T Le Bail A Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration Nucleic Acids Research 2012 40 D420 D427 10.1093/nar/gkr900
  32. Gražulis S Sarjeant A A Moeck P Stone-Sundberg J Snyder T J Kaminsky W Oliver A G Stern C L Dawe L N Rychkov D A Losev E A Boldyreva E V Tanski J M Bernstein J Rabeh W M Kantardjieff K A Crystallographic education in the 21st century Journal of Applied Crystallography 2015 48 1964 1975 10.1107/S1600576715016830
  33. Groom C R New Communications with the New CSD 2016 Available at: http://www.ccdc.cam.ac.uk/Community/blog/2016-03-15-new-communications-with-the-new-csd [Last accessed 10 April 2017]
  34. Groom C R Bruno I J Lightfoot M P Ward S C The Cambridge Structural Database Acta Crystallogr 2016 B72 171 179 10.1107/S2052520616003954
  35. Groom C R Cole J C The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery Acta Crystallogr 2017 D73 240 245 10.1107/S2059798317000675
  36. Groom C R Olsson T S G Liebeschuetz J W Bardwell D A Bruno I J Allen F H Brown N 5. Mining the Cambridge Structural Database for Bioisosteres Bioisosteres in Medicinal Chemistry 2012 Weinheim, Germany Wiley-VCH Verlag GmbH & Co. KGaA 75 101 10.1002/9783527654307.ch5
  37. Hackert M L Van Meervelt L Helliwell J R McMahon B Open Data in a Big Data World: A position paper for crystallography 2016 Chester International Union of Crystallography Available at: http://www.iucr.org/iucr/open-data [Last accessed 10 April 2017]
  38. Hall S R Allen F H Brown I D The crystallographic information file (CIF): a new standard archive file for crystallography Acta Crystallographica Section A 1991 47 655 685 10.1107/S010876739101067X
  39. Hall S R McMahon B The Implementation and Evolution of STAR/CIF Ontologies: Interoperability and Preservation of Structured Data Data Science Journal 2016 15 3 10.5334/dsj-2016-003
  40. Heller S R McNaught A Pletnev I Stein S Tchekhovskoi D InChI, the IUPAC International Chemical Identifier J. Cheminform 2015 7 23 10.1186/s13321-015-0068-4
  41. Helliwell J R Tanley S W M Preprint: Atomic resolution X-ray crystal structure of cisplatin bound to hen egg white lysozyme stored for 5 years ‘on the shelf’ 2016a 10.5281/zenodo.155068
  42. Helliwell J R Tanley S W M Raw diffraction data for atomic resolution X-ray crystal structure of cisplatin bound to hen egg white lysozyme stored for 5 years ‘on the shelf’ 2016b 10.5281/zenodo.154704
  43. Henderson R Sali A Baker M L Carragher B Devkota B Downing K H Egelman E H Feng Z Frank J Grigorieff N Jiang W Ludtke S J Medalia O Penczek P A Rosenthal P B Rossmann M G Schmid M F Schroder G F Steven A C Stokes D L Westbrook J D Wriggers W Yang H Young J Berman H M Chiu W Kleywegt G J Lawson C L Outcome of the first electron microscopy validation task force meeting Structure 2012 20 2 205 214 10.1016/j.str.2011.12.014
  44. Institut Laue Langevin ILL Data Policy 2011 Available at: https://www.ill.eu/users/ill-data-policy [Last accessed 10 April 2017]
  45. International DOI Foundation The DOI System 2017 Available at: https://www.doi.org [Last accessed 10 April 2017]
  46. International Union of Crystallography Data activities in crystallography 2017 Available at: http://www.iucr.org/resources/data [Last accessed 10 April 2017]
  47. Kabekkodu S N Faber J Fawcett T New Powder Diffraction File (PDF-4) in relational database format: advantages and data-mining capabilities Acta Crystallographica Section B: Structural Science 2002 58 333 337 10.1107/S0108768102002458
  48. Kaminsky W Snyder T Stone-Sundberg J Moeck P One-click preparation of 3D print files (*.stl, *.wrl) from *.cif (crystallographic information framework) data using Cif2VRML Powder Diffraction 2014 29 S42 S47 10.1017/s0885715614001092
  49. Karen V L Mighell A NIST Workshop on Crystallographic Databases: Preface J. Res. Natl Inst. Stand. Technol 1996 101 iii 10.6028/jres.101.001
  50. Kennard O Butterworth I From Private Data to Public Knowledge The Impact of Electronic Publishing on the Academic Community 1997 London Portland Press Ltd. 159 166
  51. Kroon-Batenburg L M J Helliwell J R McMahon B Terwilliger T C Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements IUCrJ 2017 4 87 99 10.1107/S2052252516018315
  52. Larsen S Kostorz G Publication standards for crystal structures 2011 Available at: http://www.iucr.org/home/leading-article/2011/2011-06-02 [Last accessed 10 April 2017]
  53. Le Bail A Inorganic structure prediction with GRINSP Journal of Applied Crystallography 2005 38 389 395 10.1107/S0021889805002384
  54. Lutterotti L Chateigner D Pillière H Fontugne C Full-pattern search-match using the Crystallography Open Database: an Internet tool 2015 Available at: http://www.ecole.ensicaen.fr/~chateign/danielc/abstracts/Lutterotti_abstract_RXMatiere2013_FPSM.pdf [Last accessed 10 April 2017]
  55. Meyer G R Aragão D Mudie N J Caradoc-Davies T T McGowan S Bertling P J Groenewegen D Quenette S M Bond C S Buckle A M Androulakis S Operation of the Australian Store. Synchrotron for macromolecular crystallography Acta Crystallogr 2014 D70 2510 2519 10.1107/S1399004714016174
  56. Meyer P A Data publication with the structural biology data grid supports live analysis Nature Commun 2016 7 10882 10.1038/ncomms10882
  57. Moeck P Stone-Sundberg J Snyder T J Kaminsky W Enlivening a 300 level general education class on nanoscience and nanotechnology with 3D printed crystallographic models J. Mater. Edu 2014 77 96
  58. Montelione G T Nilges M Bax A Guntert P Herrmann T Richardson J S Schwieters C D Vranken W F Vuister G W Wishart D S Berman H M Kleywegt G J Markley J L Recommendations of the wwPDB NMR Validation Task Force Structure 2013 21 9 1563 1570 10.1016/j.str.2013.07.021
  59. Narayanan B C Westbrook J Ghosh S Petrov A I Sweeney B Zirbel C L Leontis N B Berman H M The Nucleic Acid Database: new features and capabilities Nucleic Acids Res 2013 42 D114 D122 10.1093/nar/gkt980
  60. Online Dictionary of Crystallography Main Page: crystallography 2017 Available at: http://reference.iucr.org [Last accessed 10 April 2017]
  61. OpenAIRE Zenodo – New and Improved! 2017 Available at: https://www.openaire.eu/zenodo-relaunch [Last accessed 10 April 2017]
  62. Pepponi G Gražulis S Chateigner D MPOD: A Material Property Open Database linked to structural information Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms 2012 284 10 14 10.1016/j.nimb.2011.08.070
  63. Pizzi G Cepellotti A Sabatini R Marzari N Kozinsky B AiiDA: automated interactive infrastructure and database for computational science Computational Materials Science 2016 111 218 230 10.1016/j.commatsci.2015.09.013
  64. Rajan H Uchida H Bryan D Swaminathan R Downs R Hall-Wallace M Sinha A Building the American Mineralogist Crystal Structure Database: A recipe for construction of a small Internet database Geoinformatics: Data to Knowledge 2006 Geological Society of America 10.1130/2006.2397(06)
  65. Read R J Adams P D Arendall W B III Brunger A T Emsley P Joosten R P Kleywegt G J Krissinel E B Lutteke T Otwinowski Z Perrakis A Richardson J S Sheffler W H Smith J L Tickle I J Vriend G Zwart P H A new generation of crystallographic validation tools for the protein data bank Structure 2011 19 10 1395 1412 10.1016/j.str.2011.08.006
  66. Reid J R Kaduk J A Vickers M The crystal structure of trandolapril, C24H34N2O5: an example of the utility of raw data deposition in the powder diffraction file Powder Diffraction 2016 31 3 205 210 10.1017/S0885715616000294
  67. Scalfani V F Williams A J Tkachenko V Karapetyan K Pshenichnov A Hanson R M Liddle J M Bara J E Programmatic conversion of crystal structures into 3D printable files using Jmol J. Cheminform 2016 8 66 10.1186/s13321-016-0181-z
  68. Science International Open Data in a Big Data World 2015 Paris International Council for Science Available at: http://www.icsu.org/science-international/accord [Last accessed 10 April 2017]
  69. Science & Technology Facilities Council ISIS data management policy 2011 Available at: http://www.isis.stfc.ac.uk/user-office/data-policy11204.html [Last accessed 10 April 2017]
  70. Stone-Sundberg J Kaminsky W Snyder T Moeck P 3D printed models of small and large molecules, structures and morphologies of crystals, as well as their anisotropic physical properties Crystal Research and Technology 2015 50 432 441 10.1002/crat.201400469
  71. The UniProt Consortium UniProt: a hub for protein information Nucleic Acids Research 2015 43 D204 D212 10.1093/nar/gku989
  72. University of Manchester University of Manchester Research Data Management Policy 2013 Available at: http://www.library.manchester.ac.uk/using-the-library/staff/research/services/research-data-management/policy [Last accessed 10 April 2017]
  73. White P S Rodgers J R Le Page Y CRYSTMET: a database of the structures and powder patterns of metals and intermetallics Acta Crystallogr 2002 B58 343 348 10.1107/S0108768102002902
  74. Wilcox-O’Hearn Z Warner B Tahoe: The Least-authority Filesystem 2008 21 26 Available at: https://gnunet.org/sites/default/files/lafs.pdf
  75. Wishart D S Knox C Guo A C Shrivastava S Hassanali M Stothard P Chang Z Woolsey J DrugBank: a comprehensive resource for in silico drug discovery and exploration Nucleic Acids Res 2006 34 Suppl. 1 (Database issue) D668 D672 10.1093/nar/gkj067
  76. wwPDB Data correspondences between the PDB and CSD archives now available 2015 Available at: http://wwpdb.org/news/news?year=2015#29-July-2015 [Last accessed 10 April 2017]
Language: English
Page range: 38 - 38
Submitted on: Oct 14, 2016
Accepted on: Jul 4, 2017
Published on: Aug 7, 2017
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2017 Ian Bruno, Saulius Gražulis, John R Helliwell, Soorya N Kabekkodu, Brian McMahon, John Westbrook, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.