While not a direct answer to your request for bulk downloads, are you aware of BioPerl? Introduction:"If you’re a molecular biologist it’s likely that you’re interested in gene and protein sequences, and you study them in some way on a regular basis. Perhaps you’d like to try your hand at automating some of these tasks, or you’re just curious about learning more about the programming side of bioinformatics. In this HOWTO you’ll see discussions of some of the common uses of Bioperl, like sequence analysis with BLAST and retrieving sequences from public databases. You’ll also see how to write Bioperl scripts that chain these tasks together, that’s how you’ll be able to do really powerful things with Bioperl.". Perhaps worth investigating, while not a bioinformatician I know of people who have used BioPerl to work with proteins and such like. I mention this as if the data is available this way it may be a better option than having to write the code to parse various sites/pages to get the data you want.
