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Biomacromolecular Fragments and Patterns

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Structural Bioinformatics Tools for Drug Design

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

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Abstract

Structural bioinformatics is flourishing from the increased public availability of high-resolution biomacromolecular structures. Careful analysis of these models enables us to study their important structural features, such as catalytic sites, which catalyze the majority of chemical reactions in living organisms; binding sites controlling vital cell processes, and many more. As a consequence, gathering all this information together enables us to understand key biological and biochemical processes in an unprecedented level of detail. Indeed, this knowledge can be in turn adopted, not only for studying the molecular basis of uncharacterized diseases, or designing novel inhibitors, but it can also find applications in biotechnology, agriculture etc. This chapter provides an introduction to the biologically important parts of proteins which are referred to as biomacromolecular patterns or fragments, and overviews selected software tools for their identification in publicly available databases.

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Notes

  1. 1.

    Off-target protein binding implies an undesirable binding of a small molecule with a therapeutic effect to a protein target other than the primary target for which it was intended. Such binding often causes unintended side effects.

  2. 2.

    RMSD is a metric describing the structural difference between two molecules (patterns) in Ångströms, i.e. how well would two or more structures fit on top of each other. The higher the RMSD is, the more divergent the structures are. Two molecules with identical conformation (same atomic positions) have an RMSD equal to 0.

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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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  7. Michal Otyepka
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Correspondence to Jaroslav Koča .

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Koča, J. et al. (2016). Biomacromolecular Fragments and Patterns. 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_2

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