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Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins.
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
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2013 (English)In: Data Mining for Systems Biology / [ed] Hiroshi Mamitsuka, Charles DeLisi, Minoru Kanehisa, New York: Humana Press, 2013, Vol. 939, 115-140 p.Chapter in book (Refereed)
Abstract [en]

In this chapter, we first discuss protein localization in bacteria and evaluate some localization prediction tools on an independent dataset. Next, we focus on β-barrel outer membrane proteins (BOMPs), describing and evaluating new tools for BOMP detection and topology prediction. Finally, we apply general protein structure prediction methods on these proteins to show that the structure of most BOMPs in E. coli can be modeled reliably.

Place, publisher, year, edition, pages
New York: Humana Press, 2013. Vol. 939, 115-140 p.
Series
Methods in molecular biology : methods and protocols, ISSN 1064-3745 ; 939
Keyword [en]
Protein localization, Topologyprediction, β-barrelmembrane proteins, SVM, HMM
National Category
Biochemistry and Molecular Biology Cell and Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-98666DOI: 10.1007/978-1-62703-107-3_10PubMedID: 23192545Libris ID: 13975050ISBN: 978-1-62703-106-6 (print)ISBN: 978-1-62703-107-3 (print)OAI: oai:DiVA.org:su-98666DiVA: diva2:684986
Available from: 2014-01-08 Created: 2014-01-08 Last updated: 2014-11-10Bibliographically approved

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