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YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations

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Book cover Protein Engineering

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1685))

Abstract

In biocatalysis, structural knowledge regarding an enzyme and its substrate interactions complements and guides experimental investigations. Structural knowledge regarding an enzyme or a biocatalytic reaction system can be generated through computational techniques, such as homology- or molecular modeling. For this type of computational work, a computer program developed for molecular modeling of proteins is required. Here, we describe the use of the program YASARA Structure. Protocols for two specific biocatalytic applications, including both homology modeling and molecular modeling such as energy minimization, molecular docking simulations and molecular dynamics simulations, are shown. The applications are chosen to give realistic examples showing how structural knowledge through homology and molecular modeling is used to guide biocatalytic investigations and protein engineering studies.

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Acknowledgment

This work was funded by KTH Royal Institute of Technology.

Author information

Authors and Affiliations

  1. School of Biotechnology, Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91, Stockholm, Sweden

    Henrik Land & Maria Svedendahl Humble

  2. Department of Chemistry, Molecular Biomimetics, Uppsala University, Ångström Laboratory, SE-751 20, Uppsala, Sweden

    Henrik Land

  3. Pharem Biotech AB, Biovation Park, Forskargatan 20J, SE-151 36, Södertälje, Sweden

    Maria Svedendahl Humble

Authors
  1. Henrik Land
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  2. Maria Svedendahl Humble
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Corresponding author

Correspondence to Maria Svedendahl Humble .

Editor information

Editors and Affiliations

  1. Department of Biotechnology and Enzyme Catalysis Institute of Biochemistry, Greifswald University, Greifswald, Germany

    Uwe T. Bornscheuer

  2. Protein Biochemistry Institute of Biochemistry, Greifswald University, Greifswald, Germany

    Matthias Höhne

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Land, H., Humble, M.S. (2018). YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations. In: Bornscheuer, U., Höhne, M. (eds) Protein Engineering. Methods in Molecular Biology, vol 1685. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7366-8_4

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  • DOI: https://doi.org/10.1007/978-1-4939-7366-8_4

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7364-4

  • Online ISBN: 978-1-4939-7366-8

  • eBook Packages: Springer Protocols

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