Well amino acids will denature under extreme heat, but the beautiful thing about them is they are able to reconfigure at room temp. so my advice to you is go here and read some of those pancake recipes and try that out (will work equally for muffins as well)
Also, you might want to try my or Supa Freak's homemade real replacement shake. Things like peanut butter, cans of tuna, beef jerky, etc are really easy things to carry to school or work to get those calories, each are calorie dense in all the right areas. Good amounts of protein and carbs and essential fats. Best of luck.