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In Silico Laboratory: Tools for Similarity-Based Drug Discovery

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Targeting Enzymes for Pharmaceutical Development

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2089))

Abstract

Computational methods that predict and evaluate binding of ligands to receptors implicated in different pathologies have become crucial in modern drug design and discovery. Here, we describe protocols for using the recently developed package of computational tools for similarity-based drug discovery. The ProBiS stand-alone program and web server allow superimposition of protein structures against large protein databases and predict ligands based on detected binding site similarities. GenProBiS allows mapping of human somatic missense mutations related to cancer and non-synonymous single nucleotide polymorphisms and subsequent visual exploration of specific interactions in connection to these mutations. We describe protocols for using LiSiCA, a fast ligand-based virtual screening software that enables easy screening of large databases containing billions of small molecules. Finally, we show the use of BoBER, a web interface that enables user-friendly access to a large database of bioisosteric and scaffold hopping replacements.

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Acknowledgments

Financial support through Slovenian Research Agency grant L7-8269 is gratefully acknowledged.

Author information

Authors and Affiliations

  1. Faculty of Chemistry and Chemical Technology, University of Maribor, Maribor, Slovenia

    Samo Lešnik & Janez Konc

  2. National Institute of Chemistry, Ljubljana, Slovenia

    Janez Konc

  3. Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia

    Janez Konc

  4. Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia

    Janez Konc

Authors
  1. Samo Lešnik
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  2. Janez Konc
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Corresponding author

Correspondence to Janez Konc .

Editor information

Editors and Affiliations

  1. Department of Biotechnology, Agricultural University of Athens, Athens, Greece

    Nikolaos E. Labrou

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Lešnik, S., Konc, J. (2020). In Silico Laboratory: Tools for Similarity-Based Drug Discovery. In: Labrou, N. (eds) Targeting Enzymes for Pharmaceutical Development. Methods in Molecular Biology, vol 2089. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0163-1_1

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  • DOI: https://doi.org/10.1007/978-1-0716-0163-1_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0162-4

  • Online ISBN: 978-1-0716-0163-1

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