PREDICTION OF TRANSMEMBRANE ALPHA-HELICES IN PROKARYOTIC MEMBRANE-PROTEINS - THE DENSE ALIGNMENT SURFACE METHOD

A new, simple method for predicting transmembrane segments in integral membrane proteins has been developed, It is based on low-stringency d ot-plots of the query sequence against a collection of non-homologous membrane proteins using a previously derived scoring matrix [Cserzo et al., 1994, J. Mol. Biol., 243, 388-396], This so-called dense alignme nt surface (DAS) method is shown to perform on par with earlier method s that require extra information in the form of multiple sequence alig nments or the distribution of positively charged residues outside the transmembrane segments, and thus improves prediction abilities when on ly single-sequence information is available or for classes of membrane proteins that do not follow the 'positive inside' rule.