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YASARA: A Tool to Obtain Structural Guidance in Biocatalytic Investigations

  • Henrik Land
  • Maria Svedendahl HumbleEmail author
Protocol
First Online:
Part of the Methods in Molecular Biology book series (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.

Key words

Biocatalysis Enzyme Energy minimization Homology modeling Molecular modeling Molecular docking simulations Molecular dynamics simulations Protein engineering 
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Notes

Acknowledgment

This work was funded by KTH Royal Institute of Technology.

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.School of BiotechnologyIndustrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University CenterStockholmSweden
  2. 2.Department of Chemistry, Molecular BiomimeticsUppsala UniversityUppsalaSweden
  3. 3.Pharem Biotech ABSödertäljeSweden

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