Well, if you want to get a clue about how molecular biologists think you could do a lot worse then read "The eighth day of creation." It's a general history of molecular biology. If you find any of it confusing then a good introductory text book may help; Molecular Biology of the Cell or Stryer would get you started (and will be available in any decent college library).

As for the protein folding or the protein function question google around computational chemistry, but be warned -- this is tough stuff! But if you are shit hot, please come as we need the help...