Prediction of transmembrane β strands:
The polypeptide chain of cytoplasmic membrane proteins traverses the lipid bilayer in the form of α helices.
By contrast, the polypeptide chain of bacterial outer membrane proteins traverses the lipid bilayer in the form of β strands
(Koebnik et al., 2000).
Estimations using the program Hunter suggest that outer membrane proteins constitute 1.5 % to 2.4 % of the proteome of Gram-negative bacteria (Casadio et al., 2003).
Membrane-spanning β strands are less easy to predict and existing algorithms are less precise for this class of membrane proteins.
Still, some of them are listet below:
Horst Vogel and Fritz Jähnig (1986)
Models for the structure of outer-membrane proteins of Escherichia coli derived from raman spectroscopy and prediction methods
J. Mol. Biol. 190: 191-199
Tilman Schirmer and Sandra W. Cowan (1993)
Prediction of membrane-spanning beta-strands and its application to maltoporin
Protein Sci. 2: 1361-1363
Andrew F. Neuwald, Jun S. Liu, and Charles E. Lawrence (1995)
Gibbs motif sampling: detection of bacterial outer membrane protein repeats
Protein Sci. 4: 1618-1632
M. Michael Gromiha, R. Majumdar, and P.K. Ponnuswamy (1997)
Identification of membrane spanning beta strands in bacterial porins
Protein Eng. 10: 497-500
Omp_topo_predict (NN)
Kay Diederichs, Jörg Freigang, Stephan Umhau, Kornelius Zeth, and Jason Breed (1998)
Prediction by a neural network of outer membrane beta-strand protein topology
Protein Sci. 7: 2413-2420
B2TMPRED (Login)
B2TMPRED (Run)
Irene Jacoboni, Pier Luigi Martelli, Piero Fariselli, Vito De Pinto, and Rita Casadio (2001)
Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor
Protein Science 10: 779-787
William C. Wimley (2002)
Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures
Protein Sci. 11: 301-312
B2TMR / HMM-B2TMR: Topologievorhersage von Außenmembranproteinen (NN/HMM) (Home)
B2TMR / HMM-B2TMR (Login)
Pier Luigi Martelli, Piero Fariselli, Anders Krogh, and Rita Casadio (2002)
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins
Bioinformatics 18: S46-S53
BBF: Beta-Barrel Finder
Yufeng Zhai and Milton H. Saier, Jr. (2002)
The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes
Protein Sci. 11: 2196-2207
TMBETA (NN)
M. Michael Gromiha, Shandar Ahmad, and Makiko Suwa (2004)
Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins
J. Comp. Chem. 25: 762-767
M. Michael Gromiha and Makiko Suwa (2005)
A simple statistical method for discriminating outer membrane proteins with better accuracy
Bioinformatics 21: 961-968
M. Michael Gromiha, Shandar Ahmad, and Makiko Suwa (2005)
Application of residue distribution along the sequence for discriminating outer membrane proteins
Comput. Biol Chem. 29: 135-142
TMBETA-NET (NN)
M. Michael Gromiha, Shandar Ahmad, and Makiko Suwa (2005)
TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins
Nucleic Acids Res. 33: W164-W167
TBBpred (SVM)
N.K. Natt, H. Kaur, and G.P. Raghava (2004)
Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods
Proteins 56: 11-18
ProfTMB (HMM)
Henry R. Bigelow, Donald S. Petrey, Jinfeng Liu, Dariusz Przybylski, and Burkhard Rost (2004)
Predicting transmembrane beta-barrels in proteomes
Nucleic Acids Res. 32: 2566-2577