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Structural Bioinformatics Tools for Drug Design

Extraction of Biologically Relevant Information from Structural Databases

  • Jaroslav Koča
  • Radka Svobodová Vařeková
  • Lukáš Pravda
  • Karel Berka
  • Stanislav Geidl
  • David Sehnal
  • Michal Otyepka

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

Table of contents

  1. Front Matter
    Pages i-xiii
  2. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
    Pages 1-4
  3. Patterns, Fragments and Data Sources

    1. Front Matter
      Pages 5-5
    2. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 7-15
    3. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 17-30
    4. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 31-39
  4. Detection and Extraction

    1. Front Matter
      Pages 41-41
    2. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 43-57
    3. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 59-69
  5. Characterization

    1. Front Matter
      Pages 71-71
    2. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 73-80
    3. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 81-90
  6. Complete Process of Data Extraction and Analysis

    1. Front Matter
      Pages 91-91
    2. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 93-108
  7. Conclusion

    1. Front Matter
      Pages 109-109
    2. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 111-111
    3. Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal et al.
      Pages 113-140
  8. Back Matter
    Pages 141-144

About this book

Introduction

A large amount of structural data on biomacromolecules is available and the number of resolved structures is growing rapidly. This implies that we have an increasing opportunity to perform so far unprecedented analyses to obtain crucial biological insight. Biomacromolecular structural fragments such as binding sites or active sites, ligands, channels, pores, secondary structure motifs, etc., become very promising objects for these analyses because such fragments often serve as drug targets or drug templates, or substrate-specific pathways.

However, such analyses are very challenging due to their complexity and, consequently, also because they require application of a combination of different software tools. In this book, we describe individual steps necessary for analysis of biomacromolecular fragments and provide a lsit of software tools required to perform such steps. For each step, we also show corresponding web-based tools in detail and provide a few practical examples of their usage.

Keywords

detection of biomacromolecular patterns and fragments Structural bioinformatics tools databases of molecular structure drug design validation of ligands detection of channels and pores atomic charges calculation in biomacromolecules

Authors and affiliations

  • Jaroslav Koča
    • 1
  • Radka Svobodová Vařeková
    • 2
  • Lukáš Pravda
    • 3
  • Karel Berka
    • 4
  • Stanislav Geidl
    • 5
  • David Sehnal
    • 6
  • Michal Otyepka
    • 7
  1. 1.National Centre for Biomolecular ResearchMasaryk University Brno, Faculty of Science National Centre Biomolecular ResearchBrno-BohuniceCzech Republic
  2. 2.National Centre for Biomolecular ResearchMasaryk University Brno, Faculty of Science National Centre Biomolecular ResearchBrno-BohuniceCzech Republic
  3. 3.National Centre for Biomolecular ResearchMasaryk University Brno, Faculty of Science National Centre Biomolecular ResearchBrno-BohuniceCzech Republic
  4. 4.Regional Centre of Advanced Technologies and Materials, Department of Physical ChemistryPalacký University Olomouc, Faculty of Science OlomoucCzech Republic
  5. 5.National Centre for Biomolecular ResearchMasaryk University Brno, Faculty of Science National Centre Biomolecular ResearchBrno-BohuniceCzech Republic
  6. 6.National Centre for Biomolecular ResearchMasaryk University Brno, Faculty of Science National Centre Biomolecular ResearchBrno-BohuniceCzech Republic
  7. 7.Regional Centre of Advanced Technologies and Materials, Department of Physical ChemistryPalacký University Olomouc, Faculty of ScienceOlomoucCzech Republic

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-319-47388-8
  • Copyright Information The Author(s) 2016
  • Publisher Name Springer, Cham
  • eBook Packages Biomedical and Life Sciences
  • Print ISBN 978-3-319-47387-1
  • Online ISBN 978-3-319-47388-8
  • Series Print ISSN 2211-9353
  • Series Online ISSN 2211-9361
  • Buy this book on publisher's site