I've been following Atkins for three years now (fell off the bandwagon once and am 15lbs. from goal now), and protein shakes work fine for me. You have to watch the carb intake on some designer wheys though. However, I weight train seriously and am training for my second marathon. My body uses the designer whey post workout to aid in muscle recovery. If you are into intense exercise, I would recommend them to help supplement the quick burning glycogen present in muscle tissue and aid in the restorative process. If you are rather sedentary, I would follow the advice of Brook and the like and omit whey protein until after you complete induction.

You can still lose using protein shakes, bars, etc., if you are extremely active. Otherwise, you might plateau and stall your weight loss. Like Ned, I am a believer in protein shakes, Atkins forum or not. It just depends on your body type and level of activity. It's not that I can't find anything else to eat when I'm at the grocery store, I just happen to prefer these types of supplements prior to morning hillwork or a ten mile jaunt. It's fairly hard to run a 10k with a belly full of bacon and eggs. If I'm not training, I also just LIKE them, period.

You'll notice that my body fat percentages seem skewed if it says I'm still 15lbs. away from goal. That's because most of it is muscle. I credit protein shakes with my muscle mass, density, and strength, as they allow me to run long distances, lift weights, and not suffer lossage of mass like most seriously active people do while "dieting." Of course, I use the word "dieting" flippantly, as this is a WOL, not a diet. Most gym rats know you can't "diet" and expect to increase muscle strength and definition.

Experiment with yourself--if you find you stall with the whey protein, cut it until after induction. If you continue to lose at your current stats, adjust accordingly.

Most of all, good luck!