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Structural Bioinformatics Databases of General Use

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Book cover Structural Bioinformatics Tools for Drug Design

Part of the book series: SpringerBriefs in Biochemistry and Molecular Biology ((BRIEFSBIOCHEM))

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Abstract

Nowadays life sciences are filled with data gathered from many sources and these biological data are stored in many databases. Analysis of data gathered within these databases enables new view on the life from many aspects. This chapter describes several important structural bioinformatics databases which offer enormous possibilities for gathering analysis of available information about particular biomacromolecule, e.g., its 3D structure, sequence variations, annotation of function, intrinsic flexibility, ligand binding cavity identification, interactions with ligand, membrane localization, and much more. Important non-structural databases are enlisted as well to broaden the possibility of analysis. The chapter is also supplemented with several examples that illustrate the use and limitations of current structural bioinformatics databases.

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Notes

  1. 1.

    For more complete list of structural databases please refer to http://www.oxfordjournals.org/our_journals/nar/database/subcat/4/14.

  2. 2.

    Latest version of PDB format documentation can be found at http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html.

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Authors and Affiliations

  1. Faculty of Science, National Centre for Biomolecular Research, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Brno-Bohunice, Czech Republic

    Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Stanislav Geidl & David Sehnal

  2. Department of Physical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Olomouc, Czech Republic

    Karel Berka & Michal Otyepka

Authors
  1. Jaroslav Koča
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  2. Radka Svobodová Vařeková
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  3. Lukáš Pravda
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Correspondence to Jaroslav Koča .

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Koča, J. et al. (2016). Structural Bioinformatics Databases of General Use. In: Structural Bioinformatics Tools for Drug Design. SpringerBriefs in Biochemistry and Molecular Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-47388-8_3

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