Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
YASARA: A tool to obtain structural guidance in biocatalytic investigations
KTH, School of Biotechnology (BIO), Industrial Biotechnology. Uppsala University, Sweden.
KTH, School of Biotechnology (BIO), Industrial Biotechnology. Pharem Biotech AB, Sweden.
2018 (English)In: Protein Engineering: Methods and Protocols, Humana Press, 2018, Vol. 1685, 43-67 p.Chapter in book (Refereed)
Abstract [en]

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.

Place, publisher, year, edition, pages
Humana Press, 2018. Vol. 1685, 43-67 p.
Series
Methods in Molecular Biology, ISSN 1064-3745 ; 1685
Keyword [en]
Biocatalysis, Energy minimization, Enzyme, Homology modeling, Molecular docking simulations, Molecular dynamics simulations, Molecular modeling, Protein engineering
National Category
Biophysics
Identifiers
URN: urn:nbn:se:kth:diva-217482DOI: 10.1007/978-1-4939-7366-8_4PubMedID: 29086303Scopus ID: 2-s2.0-85032616567ISBN: 978-1-4939-7364-4 (print)OAI: oai:DiVA.org:kth-217482DiVA: diva2:1156847
Note

QC 20171114

Available from: 2017-11-14 Created: 2017-11-14 Last updated: 2017-11-14Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMedScopus

Search in DiVA

By author/editor
Land, HenrikSvedendahl Humble, Maria
By organisation
Industrial Biotechnology
Biophysics

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
isbn
urn-nbn

Altmetric score

doi
pubmed
isbn
urn-nbn
Total: 11 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf