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YASARA : A tool to obtain structural guidance in biocatalytic investigations
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- Land, Henrik (author)
- KTH,Industriell bioteknologi,Uppsala University, Sweden
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- Svedendahl Humble, Maria (author)
- KTH,Industriell bioteknologi,Pharem Biotech AB, Sweden
- (creator_code:org_t)
- 2017-10-31
- 2018
- English.
- In: Protein Engineering. - New York, NY : Humana Press. - 9781493973644 ; , s. 43-67
- Book chapter (peer-reviewed)
Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Biofysik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biophysics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
Keyword
- Biocatalysis
- Energy minimization
- Enzyme
- Homology modeling
- Molecular docking simulations
- Molecular dynamics simulations
- Molecular modeling
- Protein engineering
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- kap (subject category)
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