Literature DB >> 28573593

Databases, Repositories, and Other Data Resources in Structural Biology.

Heping Zheng1, Przemyslaw J Porebski1, Marek Grabowski1, David R Cooper1, Wladek Minor2.   

Abstract

Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and "meta" data with a high demand on data storage and manipulations. Primary data come from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of various biomedical problems. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) Databases, and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, as well as integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive "hubs", or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors.

Entities:  

Keywords:  Archive; Data resource; Database; Information system; Metadata; Repository; Structural biology

Mesh:

Substances:

Year:  2017        PMID: 28573593      PMCID: PMC5587190          DOI: 10.1007/978-1-4939-7000-1_27

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  83 in total

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Authors:  Lukasz Goldschmidt; David R Cooper; Zygmunt S Derewenda; David Eisenberg
Journal:  Protein Sci       Date:  2007-08       Impact factor: 6.725

Review 5.  Unmet challenges of structural genomics.

Authors:  Maksymilian Chruszcz; Marcin Domagalski; Tomasz Osinski; Alexander Wlodawer; Wladek Minor
Journal:  Curr Opin Struct Biol       Date:  2010-08-31       Impact factor: 6.809

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Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

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8.  The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.

Authors:  Margaret J Gabanyi; Paul D Adams; Konstantin Arnold; Lorenza Bordoli; Lester G Carter; Judith Flippen-Andersen; Lida Gifford; Juergen Haas; Andrei Kouranov; William A McLaughlin; David I Micallef; Wladek Minor; Raship Shah; Torsten Schwede; Yi-Ping Tao; John D Westbrook; Matthew Zimmerman; Helen M Berman
Journal:  J Struct Funct Genomics       Date:  2011-04-07

9.  The Protein Model Portal--a comprehensive resource for protein structure and model information.

Authors:  Juergen Haas; Steven Roth; Konstantin Arnold; Florian Kiefer; Tobias Schmidt; Lorenza Bordoli; Torsten Schwede
Journal:  Database (Oxford)       Date:  2013-04-26       Impact factor: 3.451

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Authors:  Fei Long; Alexei A Vagin; Paul Young; Garib N Murshudov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-12-05
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  1 in total

1.  Rapid response to emerging biomedical challenges and threats.

Authors:  Marek Grabowski; Joanna M Macnar; Marcin Cymborowski; David R Cooper; Ivan G Shabalin; Miroslaw Gilski; Dariusz Brzezinski; Marcin Kowiel; Zbigniew Dauter; Bernhard Rupp; Alexander Wlodawer; Mariusz Jaskolski; Wladek Minor
Journal:  IUCrJ       Date:  2021-03-26       Impact factor: 4.769

  1 in total

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