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
  • Paul Horton
Part of the Methods in Molecular Biology book series (MIMB, volume 939)


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.

Key words

Protein localization Topologyprediction β-barrelmembrane proteins SVM HMM 



ß -barrel assembly machine complex


bacterial ß -barrel outer membrane protein


hidden markov model


support vector machine


inside-outside-membrane profile


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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Kenichiro Imai
    • 1
    • 2
  • Sikander Hayat
    • 3
  • Noriyuki Sakiyama
    • 1
  • Naoya Fujita
    • 1
    • 4
  • Kentaro Tomii
    • 1
  • Arne Elofsson
    • 3
  • Paul Horton
    • 1
  1. 1.AIST, Computational Biology Research CenterTokyoJapan
  2. 2.Japan Society for the Promotion of ScienceTokyoJapan
  3. 3.Science for life laboratory, Department of Biochemistry and Biophysics, Stockholm Bioinformatics Center, Center for Biomembrane Research, Swedish E-science Research CenterStockholm UniversityStockholmSweden
  4. 4.Taiho Pharmaceutical CompanyIbarakiJapan

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