i have a fasta file of yeast orfs (from the SGD database) and i need to find out(predicted) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous available websites is not an option). is CATH database a place that can give me this info? (so far i struggle to recover anything that can help me from the website but perhaps i am missing something), if not what's the best way/software to go about it? surely, these predictions have been done before and there is a databse somewhere -- yeast is too much of an important organism, with a lot of information about its genome.
From comments I understood that you need to predictions in bulk. You can use API based system of JPred. They allow you to submit more than 1000 jobs per user per day. You can go through instructions step by step from their documentation. It looks simple !
Another hit I got while searching is Phyre2. I am sure there are many such servers.
in addition to Dexter's answer i found that the s2D does exactly what i need. setting up might be a bit tricky and is certainly more involved than setting JPred up but using it is easy and the output is in a nicer format.