The protein content remains the same if you cook them, but cooking will destroy a lot of the nutrients. I personally can't eat cooked eggs, i can't digest them. Just half a cooked egg will give me gas and bloating for hours. I started eating them raw last month, and i don't get ANY digestion problems! Yesterday i had 4 raw eggs, and had no digestion problems at all, but half a cooked one will give me problems, lol. If you want to eat them raw, make sure they're organic. Here's a great article on raw eggs :

http://www.mercola.com/2002/nov/13/eggs.htm