title: Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins.
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.
authors.affiliation: AIST, Computational Biology Research Center, Tokyo, Japan.
authors.forename: Kenichiro
authors.initials: K
authors.lastname: Imai
authors.forename: Sikander
authors.initials: S
authors.lastname: Hayat
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Sakiyama
authors.forename: Naoya
authors.initials: N
authors.lastname: Fujita
authors.forename: Kentaro
authors.initials: K
authors.lastname: Tomii
authors.forename: Arne
authors.initials: A
authors.lastname: Elofsson
authors.forename: Paul
authors.initials: P
authors.lastname: Horton
mesh_terms: D000465:Algorithms; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D016208:Databases, Factual; D004926:Escherichia coli / Q000378:metabolism; D006094:Gram-Positive Bacteria / Q000378:metabolism; D008958:Models, Molecular; D017433:Protein Structure, Secondary
chemical_list: D001425:Bacterial Outer Membrane Proteins