Literature DB >> 12520052

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

H Boutselakis1, D Dimitropoulos, J Fillon, A Golovin, K Henrick, A Hussain, J Ionides, M John, P A Keller, E Krissinel, P McNeil, A Naim, R Newman, T Oldfield, J Pineda, A Rachedi, J Copeland, A Sitnov, S Sobhany, A Suarez-Uruena, J Swaminathan, M Tagari, J Tate, S Tromm, S Velankar, W Vranken.   

Abstract

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

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Year:  2003        PMID: 12520052      PMCID: PMC165512          DOI: 10.1093/nar/gkg065

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  22 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Structural genomics offers high-speed look at proteins.

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4.  Discriminating between homodimeric and monomeric proteins in the crystalline state.

Authors:  H Ponstingl; K Henrick; J M Thornton
Journal:  Proteins       Date:  2000-10-01

5.  Creating the gene ontology resource: design and implementation.

Authors: 
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

6.  Database resources of the National Center for Biotechnology Information.

Authors:  D L Wheeler; C Chappey; A E Lash; D D Leipe; T L Madden; G D Schuler; T A Tatusova; B A Rapp
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

7.  Macromolecular Crystallographic Information File.

Authors:  P E Bourne; H M Berman; B McMahon; K D Watenpaugh; J D Westbrook; P M Fitzgerald
Journal:  Methods Enzymol       Date:  1997       Impact factor: 1.600

8.  PQS: a protein quaternary structure file server.

Authors:  K Henrick; J M Thornton
Journal:  Trends Biochem Sci       Date:  1998-09       Impact factor: 13.807

9.  The SWISS-PROT protein sequence data bank: current status.

Authors:  A Bairoch; B Boeckmann
Journal:  Nucleic Acids Res       Date:  1994-09       Impact factor: 16.971

10.  Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors:  W Kabsch; C Sander
Journal:  Biopolymers       Date:  1983-12       Impact factor: 2.505

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  32 in total

1.  E-MSD: an integrated data resource for bioinformatics.

Authors:  A Golovin; T J Oldfield; J G Tate; S Velankar; G J Barton; H Boutselakis; D Dimitropoulos; J Fillon; A Hussain; J M C Ionides; M John; P A Keller; E Krissinel; P McNeil; A Naim; R Newman; A Pajon; J Pineda; A Rachedi; J Copeland; A Sitnov; S Sobhany; A Suarez-Uruena; G J Swaminathan; M Tagari; S Tromm; W Vranken; K Henrick
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  The EMBL Nucleotide Sequence Database.

Authors:  Tamara Kulikova; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Kirsty Bates; Paul Browne; Alexandra van den Broek; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Maria Garcia-Pastor; Nicola Harte; Carola Kanz; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle McHale; Francesco Nardone; Ville Silventoinen; Peter Stoehr; Guenter Stoesser; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  The EMBL Nucleotide Sequence Database: major new developments.

Authors:  Guenter Stoesser; Wendy Baker; Alexandra van den Broek; Maria Garcia-Pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Francesco Nardone; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  The European Bioinformatics Institute's data resources.

Authors:  Catherine Brooksbank; Evelyn Camon; Midori A Harris; Michele Magrane; Maria Jesus Martin; Nicola Mulder; Claire O'Donovan; Helen Parkinson; Mary Ann Tuli; Rolf Apweiler; Ewan Birney; Alvis Brazma; Kim Henrick; Rodrigo Lopez; Guenter Stoesser; Peter Stoehr; Graham Cameron
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

5.  The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy.

Authors:  Maryann E Martone; Shenglan Zhang; Amarnath Gupta; Xufei Qian; Haiyun He; Diana L Price; Mona Wong; Simone Santini; Mark H Ellisman
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6.  Citing a Data Repository: A Case Study of the Protein Data Bank.

Authors:  Yi-Hung Huang; Peter W Rose; Chun-Nan Hsu
Journal:  PLoS One       Date:  2015-08-28       Impact factor: 3.240

7.  Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core.

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Journal:  J Biol Chem       Date:  2004-11-10       Impact factor: 5.157

8.  Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions.

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Journal:  J Struct Biol       Date:  2005-03       Impact factor: 2.867

Review 9.  3D electron microscopy of biological nanomachines: principles and applications.

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Journal:  Eur Biophys J       Date:  2007-07-05       Impact factor: 1.733

10.  Adding some SPICE to DAS.

Authors:  Andreas Prlić; Thomas A Down; Tim J P Hubbard
Journal:  Bioinformatics       Date:  2005-09-01       Impact factor: 6.937

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