Yes, a "New Scientist" article basically laid it out that the de-naturing of cooking makes proteins more easily digestible, so raw takes more energy from your body to digest than protein cooked well-done, which would be a lower-calorie food by the principle of [energy in] - [energy needed to digest]. It has also been shown (same article) that protein should now be calculated as 3.5 calories per gram. Trust the medical industry and gubmint to take about a decade to catch up to the news...
Chances are if you're that concerned with micro-managing your caloric intake you've got much bigger problems to deal with (dysmorphia, Adonis-complex, bulimia, etc.).