SABLE predicts solvent accessibility, secondary structure and transmembrane domains from sequence, and is available either as a web server or downloadable software. I've used the downloadable version. It gives you output like this: SECTION_SA Relative solvent accessibility prediction 0 -> fully Buried 9 -> fully Exposed 3rd line -> confidence level (scale from 0 to 9, corresponding to p=0.0 or low confidence and p=0.9 or high confidence, respectively) > 1 60 PETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPE 554303030456533120403353504400510063462525302010333415565115 445797748835446827696545584696888765325443495976545584455574 > 61 79 DLDMEDNDIIEAHREQIGG 4151554110201221233 5545445568487445533 END_SECTION Edit: The cool syntax coloring is due to BioStar, the SABLE output is just ASCII text. :-) Also, if you don't have an existing structure, you could try looking for a homology model at ModBase. You may be able to use the linked ModWeb modelling server to build one if it... - Ruchira S. Datta