I've figured out how to use protein secondary structure search
methods (like the one at Baylor) to predict where the helices and
coils are in an amino acid sequence. One sequence that I am interested
in has sequences that have been conserved back to the sea cucumber.
How do you take the next step? e.g., are there programs out there
that will predict the tertiary structure based on the pattern of
helices and strands in a sequence? Also, are there search programs
(like blastp for sequence) that will find similar structural motifs?
TIA for suggestions.