Localization prediction and structure-based in silico analysis of bacterial proteins: With emphasis on outer membrane proteins

Kenichiro Imai, Sikander Hayat, Noriyuki Sakiyama, Naoya Fujita, Kentaro Tomii, Arne Elofsson, Brice Horton Ii Paul

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationData Mining for Systems Biology
Subtitle of host publicationMethods and Protocols
EditorsHiroshi Mamitsuka, Minoru Kanehisa, Charles DeLisi
Pages115-140
Number of pages26
DOIs
Publication statusPublished - 2013 Jan 8

Publication series

NameMethods in Molecular Biology
Volume939
ISSN (Print)1064-3745

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Bacterial Proteins
Computer Simulation
Membrane Proteins
Proteins
Escherichia coli
Bacteria

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Imai, K., Hayat, S., Sakiyama, N., Fujita, N., Tomii, K., Elofsson, A., & Paul, B. H. I. (2013). Localization prediction and structure-based in silico analysis of bacterial proteins: With emphasis on outer membrane proteins. In H. Mamitsuka, M. Kanehisa, & C. DeLisi (Eds.), Data Mining for Systems Biology: Methods and Protocols (pp. 115-140). (Methods in Molecular Biology; Vol. 939). https://doi.org/10.1007/978-1-62703-107-3-10
Imai, Kenichiro ; Hayat, Sikander ; Sakiyama, Noriyuki ; Fujita, Naoya ; Tomii, Kentaro ; Elofsson, Arne ; Paul, Brice Horton Ii. / Localization prediction and structure-based in silico analysis of bacterial proteins : With emphasis on outer membrane proteins. Data Mining for Systems Biology: Methods and Protocols. editor / Hiroshi Mamitsuka ; Minoru Kanehisa ; Charles DeLisi. 2013. pp. 115-140 (Methods in Molecular Biology).
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Imai, K, Hayat, S, Sakiyama, N, Fujita, N, Tomii, K, Elofsson, A & Paul, BHI 2013, Localization prediction and structure-based in silico analysis of bacterial proteins: With emphasis on outer membrane proteins. in H Mamitsuka, M Kanehisa & C DeLisi (eds), Data Mining for Systems Biology: Methods and Protocols. Methods in Molecular Biology, vol. 939, pp. 115-140. https://doi.org/10.1007/978-1-62703-107-3-10

Localization prediction and structure-based in silico analysis of bacterial proteins : With emphasis on outer membrane proteins. / Imai, Kenichiro; Hayat, Sikander; Sakiyama, Noriyuki; Fujita, Naoya; Tomii, Kentaro; Elofsson, Arne; Paul, Brice Horton Ii.

Data Mining for Systems Biology: Methods and Protocols. ed. / Hiroshi Mamitsuka; Minoru Kanehisa; Charles DeLisi. 2013. p. 115-140 (Methods in Molecular Biology; Vol. 939).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Imai K, Hayat S, Sakiyama N, Fujita N, Tomii K, Elofsson A et al. Localization prediction and structure-based in silico analysis of bacterial proteins: With emphasis on outer membrane proteins. In Mamitsuka H, Kanehisa M, DeLisi C, editors, Data Mining for Systems Biology: Methods and Protocols. 2013. p. 115-140. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-62703-107-3-10