There are some funded projects and analyses available just for this purpose.
Structural genomics or high throughput structure projects take all available peptide sequences group them into families and make sure sequence families pointing to most likely novel folds were available.
Here are the status and target list for the joint center for structural genomics. This list is filtered by species as well as by project status.
Their analysis is availble for us to browse through. http://www1.jcsg.org/prod/newscripts/psca/help/document.cgi
Sorry this isn't so thorough. Nature also hosts Target Track, which allows several high throughput structure centers to coordinate their efforts. Each might have resources which could do your work for you.
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