predicting transmembrane regions
brutlag at genbank.BIO.NET
Sun Mar 11 19:48:14 EST 1990
There are many published algorithms for finding transmembrane
helices. My favorites in order are:
Eisenberg, D., Schwarz, E., Komaromy, M. and Wall, R. (1984).
Analysis of membrane and surface protein sequences with the
hydrophobic moment plot. J. Mol. Biol., 179, 125-142.
Rao, J. K. M. and Argos, P. (1986). A conformational preference
parameter to predict helices in integral membrane proteins. Biochim.
Biophys. Acta, 869, 197-214.
Klein, P., Kanehisa, M. I. and DeLisi, C. (1985). The detection and
classification of membrane-spanning proteins. Biochim. Biophys. Acta,
Wallace, B. A., Cascio, M. and Mielke, D. L. (1986). Evaluation of
methods for the prediction of membrane protein secondary structures.
Proc. Natl. Acad. Sci. USA, 83, 9423-9427.
Yeh, L.-S., Hunt, L. T., George, D. G. and Barker, W. C. (1987).
Searching protein sequences for potential transmembrane segments. Fed.
Proc., 46, 2232-2232.
Engelman, D. M., Steitz, T. A. and Goldman, A. (1986). Identifying
nonpolar transbilayer helices in amino acid sequences of membrane
proteins. Ann. Rev. Biophys. Biophys. Chem., 15, 321-353.
You can contact the authors for copies of their programs.
Also, the PC/Gene program contains at least three of these methods
including Eisenberg's and Rao and Argos's methods.
More information about the Proteins