STEPdb database:

The STEPdb database contains a comprehensive characterization of sub-cellular localization and topology of the Escherichia coli proteome. Current annotation is a result a multi-combinatorial analysis including existing databases, predictions of bioinformatic tools and exhaustive literature survey and manual curation. Tools for sequence similarity searches, prediction of sub-cellular location, visualization of membrane proteins topologies and protein complexes are included.

References related to STEPdb

STEPdb 2.0

• Loos, MS., Ramakrishnan, R., Vranken, W., Tsirigotaki, A., Tsare, E., Zorzini, V., De Geyter, J., Yuan, B., Tsamardinos, I., Klappa, M., Schymkowitz, J., Rousseau, F., Karamanou, S., Economou, A.
  Structural basis of the sub-cellular topology landscape of E. coli
  Submitted.

STEPdb 1.0

• Orfanoudaki, G. and Economou A. (2014)
  Proteome-wide Sub-cellular Topologies of E.coli polypeptides database (STEPdb)
  Molecular and Cellular Proteomics, 13, 3674-3687.
  [Abstract]

MatureP 1.0

• Orfanoudaki, G., Markaki, M, Chatzi, K., Tsamardinos, Y. and Economou, A. (2017)
  MatureP: secretory protein prediction exclusively through mature domain features.
  Scientific reports 7: 3263 | DOI:10.1038/s41598-017-03557-4
  [pdf]

Proteomics studies

• Orfanoudaki, G. and Economou, A. (2014)
  Proteome-wide sub-cellular Topologies of E. coli.
  Mol Cell Proteomics 13:, 3674-3687,
  PMID:25210196 doi: 10.1074/mcp.O114.041137

• Papanastasiou M, Orfanoudaki G, Koukaki M, Kountourakis N, Sardis MF, Aivaliotis M, Karamanou S, Economou A. (2013)
  The Escherichia coli peripheral inner membrane proteome.
  Mol Cell Proteomics 12:, 599-610,
  PMID:23230279 doi: 10.1074/mcp.M112.024711
  Supplemental Data: DC1

• Papanastasiou M, Orfanoudaki G, Kountourakis N, Koukaki M, Sardis MF, Aivaliotis M, Tsolis KC, Karamanou S, Economou A. (2016) ​
  Rapid label-free quantitative analysis of the E. coli BL21(DE3) inner membrane proteome
  PROTEOMICS 16, 85–97 Main Text: pdf
  Supplemental Data: pdf

Reviews

• Tsirigotaki, A., De Geyter, J., Sostaric, N., Orfanoudaki, G., Economou, A., and Karamanou, S., (2017)
  Bacterial protein export through the Sec pathway.
  Nature Reviews Microbiology 15, 21–36
  [Abstract]

• De Geyter, J., Tsirigotaki, A., Orfanoudaki, G., Zorzini, V., Economou, A., and Karamanou, S. (2016)
  Protein folding in the cell envelope of Escherichia coli.
  Nature Microbiology 1, 16107 | DOI: 10.1038/NMICROBIOL.2016.107.
  [Abstract]

• Portaliou AG, Tsolis KC, Loos MS, Zorzini V, Economou A. (2016)
  Type III Secretion: Building and Operating a Remarkable Nanomachine.
  Trends in Biochemical Sciences 41(2), 175-189 | DOI: 10.1016/j.tibs.2015.09.005.
  [Abstract]